Direct Amide Formation Between Carboxylic Acids and Amines: Mechanism and Development of Novel Catalytic Solutions

Despite the amide formation reaction being a key reaction in organic chemistry, the direct amide formation reaction is both little used and little explored. Acceptance of the feasibility and general applicability of this reaction depends upon the development of both an understanding of the mechanism of the reaction, and the design of catalysts, which can promote the reaction on a wide range of substrates and under ambient conditions. Investigations into uncatalysed direct amide formation began with calorimetric studies of the mixing of a series of carboxylic acids and amines in order to measure heat output, which has been compared with their ability to react to form carboxylate ammonium salts and amides. In order to identify which species (salt or H-bonded species) were formed, 1H NMR studies were also carried out by mixing the substrates in d8-toluene and monitoring the resulting reactions. These experiments were also compared to DFT computational studies, from which the relative merits of different mechanistic schemes for direct amide formation could be assessed. A neutral intermediate pathway, involving carboxylic acid dimerisation via mutual hydrogen bonding was found to be accessible and may explain how the direct amide formation reaction occurs. The synthesis of novel boronic acid compounds, which display the potential to act as catalysts for direct amide formation, has been attempted. Although the formation and purification of a reasonable amount of material for catalytic screening proved to be extremely difficult, progress towards the synthesis of these potential catalysts has been made. The application of direct amide formation to the synthesis of key intermediates for some economically important, commercial syntheses has been assessed. The results of these reactions display a varying degree of success and largely depend on the properties of the substrates used. Further investigations are therefore required to ensure that direct amide formation becomes a general tool for a wide range of carboxylic acid and amine partners

Assessment of oxygen plasma ashing as a pre-treatment for radiocarbon dating

This study investigates the potential of low-temperature oxygen plasma ashing as a technique for decontaminating charcoal and wood samples prior to radiocarbon dating. Plasma ashing is demonstrated to be rapid, controllable and surface-specific, and clear differences are identified in the rate of ashing in different organic materials. However, the ability of plasma ashing to selectively remove these different components is limited in heterogeneous sample matrices. This is because oxidation is confined to the immediate sample surface. Comparison of radiocarbon dates obtained from identical aliquots of contaminated ancient charcoal pre-treated by acid-base-acid (ABA), acid-base-oxidation-stepped combustion (ABOx-SC) and plasma ashing suggests that the technique performs as well as the ABA pre-treatment but does not remove as much contamination as the ABOx-SC technique. Plasma-ashing may be particularly useful in cases where sample size is limiting

Nitric Oxide-Releasing Xerogel-Based Fiber-Optic pH Sensors

A xerogel-based optical pH sensor capable of releasing low levels of nitric oxide (NO) and measuring changes in solution pH is reported. Through simple dip-coating procedures, aminoalkoxysilane-based xerogel films modified with N-diazeniumdiolate NO donor precursors and the fluorescent pH indicator seminaphthorhodamine-1 carboxylate (SNARF-1) were sequentially deposited onto optical fibers. The resulting sensors were characterized by fast and linear response to pH throughout the physiological range (pH 7.0-7.8). Real-time chemiluminescence measurements confirmed the presence of the overlying SNARF-1 containing TMOS layer did not have an inhibitory effect on N-diazeniumdiolate formation or NO release, and the NO-releasing coatings were capable of maintaining NO fluxes >0.4 pmol/cm2s up to 16 h. In vitro blood compatibility studies using porcine platelets confirmed the expected thromboresistivity of the NO-releasing xerogel coatings

Inflammatory Leiomyosarcoma and Histiocyte-rich Rhabdomyoblastic Tumor : a clinicopathological, immunohistochemical and genetic study of 13 cases, with a proposal for reclassification as Inflammatory Rhabdomyoblastic Tumor

Inflammatory leiomyosarcoma (ILMS), defined as a malignant neoplasm showing smooth muscle differentiation, a prominent inflammatory infiltrate, and near-haploidization , is a very rare soft tissue tumor with a generally favorable prognosis. The morphologic features of histiocyte-rich rhabdomyoblastic tumor (HRRMT) are similar to those of ILMS, although this lesion shows by definition a skeletal muscle phenotype. Recent gene expression profiling and immunohistochemical studies have also suggested that ILMS and HRRMT may be related. We studied the clinicopathologic, immunohistochemical and genetic features of four cases previously classified as ILMS and nine classified as HRRMT. Tumors from both groups tended to occur in the deep soft tissues of the extremities of young to middle-aged males and exhibited indolent behavior. Morphologically, all were well-circumscribed, often encapsulated, and showed a striking histiocyte-rich inflammatory infiltrate admixed with variably pleomorphic tumor cells showing spindled and epithelioid to rhabdoid morphology, eosinophilic cytoplasm, and prominent nucleoli, but few, if any, mitotic figures. Immunohistochemically, the tumor cells expressed desmin, alpha-smooth muscle actin, and the rhabdomyoblastic markers PAX7, MyoD1, and myogenin. H-caldesmon expression was absent in all cases, using the specific h-CD antibody. Karyotypic study (1 HRRMT) and genome-wide copy number analysis (7 HRRMT, OncoScan SNP assay), revealed near-haploidization in four cases, with subsequent genome doubling in one, an identical phenotype to that seen in ILMS. We propose reclassification of ILMS and HRRMT as inflammatory rhabdomyoblastic tumor , a name which accurately describes the salient morphologic and immunohistochemical features of this distinctive tumor, as well as its intermediate (rarely metastasizing) clinical behavior

Reduced bacterial adhesion to fibrinogen-coated substrates via nitric oxide release

The ability of nitric oxide (NO)-releasing xerogels to reduce fibrinogen-mediated adhesion of Staphylococcus aureus, Staphylococcus epidermidis, and Escherichia coli is described. A negative correlation was observed between NO surface flux and bacterial adhesion for each species tested. For S. aureus and E. coli, reduced adhesion correlated directly with NO flux from 0 to 30 pmol cm−2 s−1. A similar dependence for S. epidermidis was evident from 18 to 30 pmol cm−2 s−1. At a NO flux of 30 pmol cm−2 s−1, surface coverage of S. aureus, S. epidermidis, and E. coli was reduced by 96, 48, and 88%, respectively, compared to non-NO-releasing controls. Polymeric NO release was thus demonstrated to be an effective approach for significantly reducing fibrinogen-mediated adhesion of both gram-positive and gram-negative bacteria in vitro, thereby illustrating the advantage of active NO release as a strategy for inhibiting bacterial adhesion in the presence of pre-adsorbed protein

Evaluation of alternative solvents in common amide coupling reactions : replacement of dichloromethane and N,N-dimethylformamide

A range of alternative solvents have been evaluated within amidation reactions employing common coupling reagents with a view to identifying suitable replacements for dichloromethane and N,N-dimethylformamid

Functionally heterogeneous human satellite cells identified by single cell RNA sequencing.

Although heterogeneity is recognized within the murine satellite cell pool, a comprehensive understanding of distinct subpopulations and their functional relevance in human satellite cells is lacking. We used a combination of single cell RNA sequencing and flow cytometry to identify, distinguish, and physically separate novel subpopulations of human PAX7+ satellite cells (Hu-MuSCs) from normal muscles. We found that, although relatively homogeneous compared to activated satellite cells and committed progenitors, the Hu-MuSC pool contains clusters of transcriptionally distinct cells with consistency across human individuals. New surface marker combinations were enriched in transcriptional subclusters, including a subpopulation of Hu-MuSCs marked by CXCR4/CD29/CD56/CAV1 (CAV1+). In vitro, CAV1+ Hu-MuSCs are morphologically distinct, and characterized by resistance to activation compared to CAV1- Hu-MuSCs. In vivo, CAV1+ Hu-MuSCs demonstrated increased engraftment after transplantation. Our findings provide a comprehensive transcriptional view of normal Hu-MuSCs and describe new heterogeneity, enabling separation of functionally distinct human satellite cell subpopulations

Fragile DNA Repair Mechanism Reduces Ageing in Multicellular Model

DNA damages, as well as mutations, increase with age. It is believed that these result from increased genotoxic stress and decreased capacity for DNA repair. The two causes are not independent, DNA damage can, for example, through mutations, compromise the capacity for DNA repair, which in turn increases the amount of unrepaired DNA damage. Despite this vicious circle, we ask, can cells maintain a high DNA repair capacity for some time or is repair capacity bound to continuously decline with age? We here present a simple mathematical model for ageing in multicellular systems where cells subjected to DNA damage can undergo full repair, go apoptotic, or accumulate mutations thus reducing DNA repair capacity. Our model predicts that at the tissue level repair rate does not continuously decline with age, but instead has a characteristic extended period of high and non-declining DNA repair capacity, followed by a rapid decline. Furthermore, the time of high functionality increases, and consequently slows down the ageing process, if the DNA repair mechanism itself is vulnerable to DNA damages. Although counterintuitive at first glance, a fragile repair mechanism allows for a faster removal of compromised cells, thus freeing the space for healthy peers. This finding might be a first step toward understanding why a mutation in single DNA repair protein (e.g. Wrn or Blm) is not buffered by other repair proteins and therefore, leads to severe ageing disorders