Rapid diagnosis and severity scale of post-COVID condition using advanced spectroscopy.

The COVID-19 pandemic has resulted in a persistent health challenge known as Post-COVID Condition (PCC), characterized by symptoms lasting at least three months after the initial SARS-CoV-2 infection and potentially persisting for several years. While studies on PCC using lipidomics and proteomics have been conducted, these methods are costly and time-consuming. The comprehensive analysis of UV-VIS-NIR-MIR spectroscopy is explored here as an alternative for the rapid and cheap diagnosis and quantification of the severity of PCC.

Proteomic analysis of post-COVID condition: Insights from plasma and pellet blood fractions.

Background: Persistent symptoms extending beyond the acute phase of SARS-CoV-2 infection, known as Post-COVID condition (PCC), continue to impact many individuals years after the COVID-19 pandemic began. This highlights an urgent need for a deeper understanding and effective treatments. While significant progress has been made in understanding the acute phase of COVID-19 through omics-based approaches, the proteomic alterations linked to the long-term effects of the infection remain underexplored.

Classical Simulations on Quantum Computers: Interface-Driven Peptide Folding on Simulated Membrane Surfaces.

Background: Antimicrobial peptides (AMPs) are crucial in the fight against infections and play significant roles in various health contexts, including cancer, autoimmune diseases, and aging. A key aspect of AMP functionality is their selective interaction with pathogen membranes, which often exhibit altered lipid compositions. These interactions are thought to induce a conformational shift in AMPs from random coil to alpha-helical structures, essential for their lytic activity.

Simulating Bacterial Membrane Models at the Atomistic Level: A Force Field Comparison.

Molecular dynamics (MD) simulations are currently an indispensable tool to understand both the dynamic and nanoscale organization of cell membrane models. A large number of quantitative parameters can be extracted from these simulations, but their reliability is determined by the quality of the employed force field and the simulation parameters. Much of the work on parametrizing and optimizing force fields for biomembrane modeling has been focused on homogeneous bilayers with a single phospholipid type.

CYCLOPEp Builder: Facilitating cyclic peptide and nanotube research through a user-friendly web platform.

The study of cyclic peptides (CPs) and self-assembling cyclic peptide nanotubes (SCPNs) is pivotal in advancing applications in diverse fields such as biomedicine, nanoelectronics, and catalysis. Recognizing the limitations in the experimental study of these molecules, this article introduces CYCLOPEp Builder, a comprehensive web-based application designed to facilitate the design, simulation, and visualization of CPs and SCPNs. The tool is engineered to generate molecular topologies, essential for conducting Molecular Dynamics simulations that span All-Atom to Coarse-Grain resolutions.

Transcription factor roles in the local adaptation to temperature in the Andean Spiny Toad Rhinella spinulosa.

Environmental temperature strongly influences the adaptation dynamics of amphibians, whose limited regulation capabilities render them susceptible to thermal oscillations. A central element of the adaptive strategies is the transcription factors (TFs), which act as master regulators that orchestrate stress responses, enabling species to navigate the fluctuations of their environment skillfully. Our study delves into the intricate relationship between TF expression and thermal adaptation mechanisms in the Rhinella spinulosa populations.

Unlocking the specificity of antimicrobial peptide interactions for membrane-targeted therapies.

Antimicrobial peptides (AMPs) are increasingly recognized as potent therapeutic agents, with their selective affinity for pathological membranes, low toxicity profile, and minimal resistance development making them particularly attractive in the pharmaceutical landscape. This study offers a comprehensive analysis of the interaction between specific AMPs, including magainin-2, pleurocidin, CM15, LL37, and clavanin, with lipid bilayer models of very different compositions that have been ordinarily used as biological membrane models of healthy mammal, cancerous, and bacterial cells. Employing unbiased molecular dynamics simulations and metadynamics techniques, we have deciphered the intricate mechanisms by which these peptides recognize pathogenic and pathologic lipid patterns and integrate into lipid assemblies.

Unraveling the molecular dynamics of sugammadex-rocuronium complexation: A blueprint for cyclodextrin drug design.

Sugammadex, marketed as Bridion™, is an approved cyclodextrin (CD) based drug for the reversal of neuromuscular blockade in adults undergoing surgery. Sugammadex forms an inclusion complex with the neuromuscular blocking agent (NMBA) rocuronium, allowing rapid reversal of muscle paralysis. In silico methods have been developed for studying CD inclusion complexes, aimed at accurately predicting their structural, energetic, dynamic, and kinetic properties, as well as binding constants.

Cyclodextrins: Establishing building blocks for AI-driven drug design by determining affinity constants .

Cyclodextrins (CDs) are cyclic carbohydrate polymers that hold significant promise for drug delivery and industrial applications. Their effectiveness depends on their ability to encapsulate target molecules with strong affinity and specificity, but quantifying affinities in these systems accurately is challenging for a variety of reasons. Computational methods represent an exceptional complement to assays because they can be employed for existing and hypothetical molecules, providing high resolution structures in addition to a mechanistic, dynamic, kinetic, and thermodynamic characterization.

Lipidomics signature in post-COVID patient sera and its influence on the prolonged inflammatory response.

Background: The ongoing issues with post-COVID conditions (PCC), where symptoms persist long after the initial infection, highlight the need for research into blood lipid changes in these patients. While most studies focus on the acute phase of COVID-19, there's a significant lack of information on the lipidomic changes that occur in the later stages of the disease. Addressing this knowledge gap is critical for understanding the long-term effects of COVID-19 and could be key to developing personalized treatments for those suffering from PCC.

Unraveling lipid and inflammation interplay in cancer, aging and infection for novel theranostic approaches.

The synergistic relationships between Cancer, Aging, and Infection, here referred to as the CAIn Triangle, are significant determinants in numerous health maladies and mortality rates. The CAIn-related pathologies exhibit close correlations with each other and share two common underlying factors: persistent inflammation and anomalous lipid concentration profiles in the membranes of affected cells. This study provides a comprehensive evaluation of the most pertinent interconnections within the CAIn Triangle, in addition to examining the relationship between chronic inflammation and specific lipidic compositions in cellular membranes.

Overlay databank unlocks data-driven analyses of biomolecules for all.

Tools based on artificial intelligence (AI) are currently revolutionising many fields, yet their applications are often limited by the lack of suitable training data in programmatically accessible format. Here we propose an effective solution to make data scattered in various locations and formats accessible for data-driven and machine learning applications using the overlay databank format. To demonstrate the practical relevance of such approach, we present the NMRlipids Databank-a community-driven, open-for-all database featuring programmatic access to quality-evaluated atom-resolution molecular dynamics simulations of cellular membranes.

An outsider on the Antarctic Peninsula: A new record of the non-native moth (Lepidoptera: Pyralidae).

We report the first record of the microlepidopteran beyond the South Shetland Islands at the Chilean Yelcho scientific station (64°52'33.1428″ S; 63°35'1.9572″ W), Doumer Island, close to the west coast of the Antarctic Peninsula.

Treatment effect of ex vivo expanded allogeneic bone marrow-derived mesenchymal stem cells for the treatment of fistulizing Crohn's disease are durable at 12 months.

Background: Mesenchymal stem cells have been administered via direct injection to treat perianal Crohn's fistulizing disease. We herein sought to determine the safety and durability of treatment response to 12 months with 3 individual phase IB/IIA clinical trials of mesenchymal stem cells for refractory perianal, rectovaginal, and ileal pouch fistulas in the setting of Crohn disease.

Methods: Three phase IB/IIA randomized placebo-controlled single-blinded clinical trials were performed for (1) perianal fistulas, (2) rectovaginal fistula, and (3) ileal pouch in situ with anovaginal and/or perianal fistulas.

Addressing the complexities in measuring cyclodextrin-sterol binding constants: A multidimensional study.

A class of cyclodextrin (CD) dimers has emerged as a potential new treatment for atherosclerosis; they work by forming strong, soluble inclusion complexes with oxysterols, allowing the body to reduce and heal arterial plaques. However, characterizing the interactions between CD dimers and oxysterols presents formidable challenges due to low sterol solubility, the synthesis of modified CDs resulting in varying number and position of molecular substitutions, and the diversity of interaction mechanisms. To address these challenges and illuminate the nuances of CD-sterol interactions, we have used multiple orthogonal approaches for a comprehensive characterization.

A phase IB/IIA study of ex vivo expanded allogeneic bone marrow-derived mesenchymal stem cells for the treatment of rectovaginal fistulizing Crohn's disease.

Background: Crohn-related rectovaginal fistulas are notoriously difficult to treat. Studies of mesenchymal stem cells for the treatment of perianal Crohn fistulizing disease have largely excluded rectovaginal fistulas. The aim of this study was to determine the safety and efficacy of mesenchymal stem cells for refractory rectovaginal fistulizing Crohn disease.

Molecular insights into the effects of focused ultrasound mechanotherapy on lipid bilayers: Unlocking the keys to design effective treatments.

Administration of focused ultrasounds (US) represents an attractive complement to classical therapies for a wide range of maladies, from cancer to neurological pathologies, as they are non-invasive, easily targeted, their dosage is easy to control, and they involve low risks. Different mechanisms have been proposed for their activity but the direct effect of their interaction with cell membranes is not well understood at the molecular level. This is in part due to the difficulty of designing experiments able to probe the required spatio-temporal resolutions.

Multiple clonal transmissions of clinically relevant extended-spectrum beta-lactamase-producing Escherichia coli among livestock, dogs, and wildlife in Chile.

Objectives: Extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli) are a main cause of human deaths associated with antimicrobial resistance (AMR). Despite hundreds of reports of the faecal carriage of ESBL-E.

The Role of AI in Drug Discovery: Challenges, Opportunities, and Strategies.

Artificial intelligence (AI) has the potential to revolutionize the drug discovery process, offering improved efficiency, accuracy, and speed. However, the successful application of AI is dependent on the availability of high-quality data, the addressing of ethical concerns, and the recognition of the limitations of AI-based approaches. In this article, the benefits, challenges, and drawbacks of AI in this field are reviewed, and possible strategies and approaches for overcoming the present obstacles are proposed.

Evaluating the functional, sexual and seasonal variation in the chemical constituents from feces of adult Iberian wolves (Canis lupus signatus).

Chemical signals deposited in feces play an important role in intraspecific and interspecific communication of many mammals. We collected fresh feces of adult wolves from wild breeding groups. All samples visually identified as belonging to wolves were subsequently identified to species level by sequencing a small fragment of mtDNA and sexed typing DBX6 and DBY7 sex markers.

Uncovering the mechanisms of cyclic peptide self-assembly in membranes with the chirality-aware MA(R/S)TINI forcefield.

Cyclic peptides (CPs) formed by alternation of D- and L-amino acids (D,L-CPs) can self-assemble into nanotubes (SCPNs) by parallel or/and antiparallel stacking. Different applications have been attributed to these nanotubes, including the disruption of lipid bilayers of specific compositions and the selective transport of ions throughout membranes. Molecular dynamics (MD) simulations have significantly contributed to understand the interaction between CPs, including the structural, dynamic and transport properties of their supramolecular aggregates.

A Phase IB/IIA Study of Allogeneic, Bone Marrow-derived, Mesenchymal Stem Cells for the Treatment of Refractory Ileal-anal Anastomosis and Peripouch Fistulas in the Setting of Crohn's Disease of the Pouch.

Background And Aims: Mesenchymal stem cells [MSCs] have been used for the treatment of perianal Crohn's fistulising disease by direction injection. No studies to date have included patients with an ileal pouch-anal anastomosis [IPAA] in situ.

Methods: A phase IB/IIA, randomised, control trial of bone marrow-derived, allogeneic MSCs via direct injection to treat adult patients with a peripouch fistula[s] was conducted; 75 million MSCs were administered with a 22 G needle, with repeat injection at 3 months if complete clinical and radiographic healing was not achieved.

Dynamically Induced Symmetry Breaking and Out-of-Equilibrium Topology in a 1D Quantum System.

Nontrivial topology in lattices is characterized by invariants-such as the Zak phase for one-dimensional (1D) lattices-derived from wave functions covering the Brillouin zone. We realize the 1D bipartite Rice-Mele (RM) lattice using ultracold ^{87}Rb and focus on lattice configurations possessing various combinations of chiral, time-reversal, and particle-hole symmetries. We quench between configurations and use a form of quantum state tomography, enabled by diabatically tuning lattice parameters, to directly follow the time evolution of the Zak phase as well as a chiral winding number.