Systematic comparison of quantity and quality of RNA recovered with commercial FFPE tissue extraction kits.

Background: FFPE tissue samples are commonly used in biomedical research and are a valuable source for next-generation sequencing in oncology, however, extracting RNA from these samples can be difficult the quantity and quality achieved can impact the downstream analysis. This study compared the effectiveness of seven different commercially available RNA extraction kits specifically designed for use with FFPE samples in terms of the quantity and quality of RNA recovered.

Methods: This study used 9 samples of FFPE tissue from three different types of tissue (Tonsil, Appendix and lymph node of B-cell lymphoma) to evaluate RNA extraction methods.

Modulation of SLFN11 induces changes in DNA Damage response in breast cancer.

Background: Lack of Schlafen family member 11 (SLFN11) expression has been recently identified as a dominant genomic determinant of response to DNA damaging agents in numerous cancer types. Thus, several strategies aimed at increasing SLFN11 are explored to restore chemosensitivity of refractory cancers. In this study, we examined various approaches to elevate SLFN11 expression in breast cancer cellular models and confirmed a corresponding increase in chemosensitivity with using the most successful efficient one.

An integrated tumor, immune and microbiome atlas of colon cancer.

The lack of multi-omics cancer datasets with extensive follow-up information hinders the identification of accurate biomarkers of clinical outcome. In this cohort study, we performed comprehensive genomic analyses on fresh-frozen samples from 348 patients affected by primary colon cancer, encompassing RNA, whole-exome, deep T cell receptor and 16S bacterial rRNA gene sequencing on tumor and matched healthy colon tissue, complemented with tumor whole-genome sequencing for further microbiome characterization. A type 1 helper T cell, cytotoxic, gene expression signature, called Immunologic Constant of Rejection, captured the presence of clonally expanded, tumor-enriched T cell clones and outperformed conventional prognostic molecular biomarkers, such as the consensus molecular subtype and the microsatellite instability classifications.

Solid-State F NMR Chemical Shift in Square-Planar Nickel-Fluoride Complexes Linked by Halogen Bonds.

The halogen bond (XB) is a highly directional class of noncovalent interactions widely explored by experimental and computational studies. However, the NMR signature of the XB has attracted limited attention. The prediction and analysis of the solid-state NMR (SSNMR) chemical shift tensor provide useful strategies to better understand XB interactions.

AMOEBA Polarizable Force Field for Molecular Dynamics Simulations of Glyme Solvents.

Classical molecular dynamics (MD) simulations of electrolyte systems are important to gain insight into the atom-scale properties that determine the battery-relevant performance. The recent Tinker-HP software release enables efficient and accurate MD simulations with the AMOEBA polarizable force field. In this work, we developed a procedure to construct a universal AMOEBA model for the solvent family of glymes (glycol methyl ethers), which involves a refinement scheme for valence parameters by fitting the AMOEBA-derived atomic forces to those computed at the DFT level.

Calcium-catalysed synthesis of amines through imine hydrosilylation: an experimental and theoretical study.

A method to reduce aldimines through hydrosilylation is reported. The catalytic system involves calcium triflimide (Ca(NTf)) and potassium hexafluorophosphate (KPF) which have been shown to act in a synergistic manner. The expected amines are obtained in fair to very high yields (40-99%) under mild conditions (room temperature in most cases).

Surface Modification of Polytetrafluoroethylene and Polycaprolactone Promoting Cell-Selective Adhesion and Growth of Valvular Interstitial Cells.

Tissue engineering concepts, which are concerned with the attachment and growth of specific cell types, frequently employ immobilized ligands that interact preferentially with cell types of interest. Creating multicellular grafts such as heart valves calls for scaffolds with spatial control over the different cells involved. Cardiac heart valves are mainly constituted out of two cell types, endothelial cells and valvular interstitial cells.

The immune landscape of solid pediatric tumors.

Background: Large immunogenomic analyses have demonstrated the prognostic role of the functional orientation of the tumor microenvironment in adult solid tumors, this variable has been poorly explored in the pediatric counterpart.

Methods: We performed a systematic analysis of public RNAseq data (TARGET) for five pediatric tumor types (408 patients): Wilms tumor (WLM), neuroblastoma (NBL), osteosarcoma (OS), clear cell sarcoma of the kidney (CCSK) and rhabdoid tumor of the kidney (RT). We assessed the performance of the Immunologic Constant of Rejection (ICR), which captures an active Th1/cytotoxic response.

In vitro Interleukin-7 treatment partially rescues MAIT cell dysfunction caused by SARS-CoV-2 infection.

MAIT cells have been shown to be activated upon several viral infections in a TCR-independent manner by responding to inflammatory cytokines secreted by antigen-presenting cells. Recently, a few studies have shown a similar activation of MAIT cells in response to severe acute respiratory coronavirus 2 (SARS-CoV-2) infection. In this study, we investigate the effect of SARS-CoV-2 infection on the frequency and phenotype of MAIT cells by flow cytometry, and we test in vitro stimulation conditions on the capacity to enhance or rescue the antiviral function of MAIT cells from patients with coronavirus disease 2019 (COVID-19).

P Chemical Shifts in Ru(II) Phosphine Complexes. A Computational Study of the Influence of the Coordination Sphere.

The NMR chemical shift has been the most versatile marker of chemical structures, by reflecting global and local electronic structures, and is very sensitive to any change within the chemical species. In this work, Ru(II) complexes with the same five ligands and a variable sixth ligand L (none, HO, HS, CHSH, H, N, NO, NO, C═CHPh, and CO) are studied by using as the NMR reporter the phosphorus P of a coordinated bidentate P-N ligand (P-N = -diphenylphosphino-,'-dimethylaniline). The chemical shift of P in RuCl(P-N)(PR)(L) (R = phenyl, -tolyl, or -FCH) was shown to increase as the Ru-P bond distance decreases, an observation that was not rationalized.

Manipulation of cellular behaviour on surface-modified polyvinylidene difluoride using wet chemistry.

The surface modification of polyvinylidene difluoride (PVDF) for various biomedical uses is notoriously hampered by the chemical inertness of the polymer. A wet chemical approach aiming at covalently grafting biomolecules was demonstrated by means of an elimination reaction of fluorine from the polymer backbone followed by subsequent modification steps. Exemplified as a possible biological application, the coupling of the peptide REDV rendered the material adhesive for endothelial cells while adhesion of thrombocytes was dramatically reduced.

Efficient alkene hydrosilation with bis(8-quinolyl)phosphine (NPN) nickel catalysts. The dominant role of silyl-over hydrido-nickel catalytic intermediates.

A cationic nickel complex of the bis(8-quinolyl)(3,5-di--butylphenoxy)phosphine (NPN) ligand, [(NPN)NiCl], is a precursor to efficient catalysts for the hydrosilation of alkenes with a variety of hydrosilanes under mild conditions and low catalyst loadings. DFT studies reveal the presence of two coupled catalytic cycles based on [(NPN)NiH] and [(NPN)NiSiR] active species, with the latter being more efficient for producing the product. The preferred silyl-based catalysis is not due to a more facile insertion of alkene into the Ni-Si ( Ni-H) bond, but by consistent and efficient conversions of the hydride to the silyl complex.

Flow-Cytometry Platform for Intracellular Detection of FVIII in Blood Cells: A New Tool to Assess Gene Therapy Efficiency for Hemophilia A.

Detection of factor VIII (FVIII) in cells by flow cytometry is controversial, and no monoclonal fluorescent antibody is commercially available. In this study, we optimized such an assay and successfully used it as a platform to study the functional properties of phosphoglycerate kinase (PGK)-FVIII lentiviral vector-transduced cells by directly visualizing FVIII in cells after different gene transfer conditions. We could measure cellular stress parameters after transduction by correlating gene expression and protein accumulation data.

The march of pluripotent stem cells in cardiovascular regenerative medicine.

Cardiovascular disease (CVD) continues to be the leading cause of global morbidity and mortality. Heart failure remains a major contributor to this mortality. Despite major therapeutic advances over the past decades, a better understanding of molecular and cellular mechanisms of CVD as well as improved therapeutic strategies for the management or treatment of heart failure are increasingly needed.

Molecular and Silica-Supported Molybdenum Alkyne Metathesis Catalysts: Influence of Electronics and Dynamics on Activity Revealed by Kinetics, Solid-State NMR, and Chemical Shift Analysis.

Molybdenum-based molecular alkylidyne complexes of the type [MesC≡Mo{OC(CH)(CF)}] (MoF, x = 0; MoF, x = 1; MoF, x = 2; MoF, x = 3; Mes = 2,4,6-trimethylphenyl) and their silica-supported analogues are prepared and characterized at the molecular level, in particular by solid-state NMR, and their alkyne metathesis catalytic activity is evaluated. The C NMR chemical shift of the alkylidyne carbon increases with increasing number of fluorine atoms on the alkoxide ligands for both molecular and supported catalysts but with more shielded values for the supported complexes. The activity of these catalysts increases in the order MoF < MoF < MoF before sharply decreasing for MoF, with a similar effect for the supported systems (MoF ≈ MoF < MoF < MoF).

Metathesis Activity Encoded in the Metallacyclobutane Carbon-13 NMR Chemical Shift Tensors.

Metallacyclobutanes are an important class of organometallic intermediates, due to their role in olefin metathesis. They can have either planar or puckered rings associated with characteristic chemical and physical properties. Metathesis active metallacyclobutanes have short M-C and M···C distances, long C-C bond length, and isotropic C chemical shifts for both early d and late d transition metal compounds for the α- and β-carbons appearing at ca.

Orbital Analysis of Carbon-13 Chemical Shift Tensors Reveals Patterns to Distinguish Fischer and Schrock Carbenes.

Fischer and Schrock carbenes display highly deshielded carbon chemical shifts (>250 ppm), in particular Fischer carbenes (>300 ppm). Orbital analysis of the principal components of the chemical shift tensors determined by solid-state NMR spectroscopy and calculated by a 2-component DFT method shows specific patterns that act as fingerprints for each type of complex. The calculations highlight the role of the paramagnetic term in the shielding tensor especially in the two most deshielded components (σ and σ ).

Analysis of RBC-microparticles in stored whole blood bags - a promising marker to detect blood doping in sports?

Blood doping in sports is prohibited by the World Anti-Doping Agency (WADA). To find a possible biomarker for the detection of blood doping, we investigated the changes in blood stored in CPDA-1 blood bags of eight healthy subjects who donated one unit of blood. Aliquots were taken on days 0, 14, and 35.

Computation provides chemical insight into the diverse hydride NMR chemical shifts of [Ru(NHC)(L)H] species (NHC = N-heterocyclic carbene; L = vacant, H, N, CO, MeCN, O, P, SO, H, F and Cl) and their [Ru(RPCHCHPR)(L)H] congeners.

Relativistic density functional theory calculations, both with and without the effects of spin-orbit coupling, have been employed to model hydride NMR chemical shifts for a series of [Ru(NHC)(L)H] species (NHC = N-heterocyclic carbene; L = vacant, H, N, CO, MeCN, O, P, SO, H, F and Cl), as well as selected phosphine analogues [Ru(RPCHCHPR)(L)H] (R = Pr, Cy; L = vacant, O). Inclusion of spin-orbit coupling provides good agreement with the experimental data. For the NHC systems large variations in hydride chemical shift are shown to arise from the paramagnetic term, with high net shielding (L = vacant, Cl, F) being reinforced by the contribution from spin-orbit coupling.

Valve Tissue Engineering with Living Absorbable Threads.

Tissue engineering (TE) depends on the population of scaffolds with appropriate cells, arranged in a specific physiological direction using a variety of techniques. Here, a novel technique of creating "living threads" is described based on thin (poly(ε-caprolactone) fibers of different diameters (23-243 μm). The fibers readily attract human mesenchymal stem cells (MSCs), which are firmly adhered.

Tailoring Novel PTFE Surface Properties: Promoting Cell Adhesion and Antifouling Properties via a Wet Chemical Approach.

Many biomaterials used for tissue engineering applications lack cell-adhesiveness and, in addition, are prone to nonspecific adsorption of proteins. This is especially important for blood-contacting devices such as vascular grafts and valves where appropriate surface properties should inhibit the initial attachment of platelets and promote endothelial cell colonization. As a consequence, the long-term outcome of the implants would be improved and the need for anticoagulation therapy could be reduced or even abolished.

Maturation of pluripotent stem cell derived cardiomyocytes: The new challenge.

Stem cell therapy appears to be a promising area of research for cardiac regeneration following ischemic heart failure. However, differentiation of cardiomyocytes from pluripotent stem cells, or directly from somatic cells, leads to generation of "immature" cardiomyocytes that differ from their adult counterparts in various ways. This immaturity triggers some challenges for their potential clinical use, and multiple techniques reviewed here have been developed for maturation of those cells.