Microbial Necromass in Soils—Linking Microbes to Soil Processes and Carbon Turnover

The organic matter of living plants is the precursor material of the organic matter stored in terrestrial soil ecosystems. Although a great deal of knowledge exists on the carbon turnover processes of plant material, some of the processes of soil organic matter (SOM) formation, in particular from microbial necromass, are still not fully understood. Recent research showed that a larger part of the original plant matter is converted into microbial biomass, while the remaining part in the soil is modified by extracellular enzymes of microbes. At the end of its life, microbial biomass contributes to the microbial molecular imprint of SOM as necromass with specific properties. Next to appropriate environmental conditions, heterotrophic microorganisms require energy-containing substrates with C, H, O, N, S, P, and many other elements for growth, which are provided by the plant material and the nutrients contained in SOM. As easily degradable substrates are often scarce resources in soil, we can hypothesize that microbes optimize their carbon and energy use. Presumably, microorganisms are able to mobilize biomass building blocks (mono and oligomers of fatty acids, amino acids, amino sugars, nucleotides) with the appropriate stoichiometry from microbial necromass in SOM. This is in contrast to mobilizing only nutrients and consuming energy for new synthesis from primary metabolites of the tricarboxylic acid cycle after complete degradation of the substrates. Microbial necromass is thus an important resource in SOM, and microbial mining of building blocks could be a life strategy contributing to priming effects and providing the resources for new microbial growth cycles. Due to the energy needs of microorganisms, we can conclude that the formation of SOM through microbial biomass depends on energy flux. However, specific details and the variability of microbial growth, carbon use and decay cycles in the soil are not yet fully understood and linked to other fields of soil science. Here, we summarize the current knowledge on microbial energy gain, carbon use, growth, decay, and necromass formation for relevant soil processes, e. g. the microbial carbon pump, C storage, and stabilization. We highlight the factors controlling microbial necromass contribution to SOM and the implications for soil carbon use efficiency (CUE) and we identify research needs for process-based SOM turnover modelling and for understanding the variability of these processes in various soil types under different climates.

A comparison of aleurone cells in centenarian African and contemporary barley seeds to identify the geographic origin

Barley (Hordeum vulgare L.) is one of the main domesticated cereals. For this reason, barley seeds have been found in numerous archaeological sites, and since the mid-19th century have been available in numerous natural museum collections. About a hundred years ago samples were collected in the African countries of Eritrea and Cyrenaica (now Libya), and have been preserved as ex-situ in the museum collection “L’Orientale” of the University of Naples. The varieties of contemporary barley selected for comparative analysis were grown in Tuscany and are used in the production of craft beer. To ascertain their vitality, the ancient and contemporary seeds were placed in Petri dishes to hydrate under a sterile hood at room temperature after a sterilization procedure. Morphological and ultrastructural observations performed on the aleurone cells of the ancient samples presented vital cells. The extraction and purification of DNA from seeds produced results while the genotype comparison of ancient and contemporary barley varieties enabled the construction of a dendrogram of similarity, useful in describing barley from museum genetic heritage collections and in providing a molecular imprint of extant varieties.

Molecular imprint of epithelial origin identifies immuno-subtype of thymic epithelial tumors

Thymic epithelial tumors (TETs) are common tumors in human anterior mediastinum with limited biological understanding. Through decoding the immune landscape of tumors, we reclassify TETs into three types based on T cell developmental patterns. We uncover the developmental dysfunction and TCR repertoire of tumor-infiltrating T cells by cell atlas. Moreover, we identify the unique subset of tumor cells with distinct epithelial origin in each TETs type. Furthermore, we demonstrate that KRT14/GNB3+ mTECs-like cell accumulation inhibits the T cell positive selection in type 1 TETs, while CCL25+ cTEC-like cell promotes T cell positive selection in type 2. Interestingly, although CHI3L1+ mTEC-like cell in type 3 TETs loses the function of supporting T cell development, it acquires the capacity to induce CD8+TRMs-mediated response. Finally, we propose a new molecular classification of human TETs using GNB3 and CHI3L1 to distinguish the epithelial origin of tumor cells, which is promising in prognostic prediction.

Contribution to the Understanding of the Interaction between a Polydopamine Molecular Imprint and a Protein Model: Ionic Strength and pH Effect Investigation

Several studies were devoted to the design of molecularly imprinted polymer (MIP)-based sensors for the detection of a given protein. Here, we bring elements that could contribute to the understanding of the interaction mechanism involved in the recognition of a protein by an imprint. For this purpose, a polydopamine (PDA)-MIP was designed for bovine serum albumin (BSA) recognition. Prior to BSA grafting, the gold surfaces were functionalized with mixed self-assembled monolayers of (MUDA)/(MHOH) (1/9, v/v). The MIP was then elaborated by dopamine electropolymerization and further extraction of BSA templates by incubating the electrode in proteinase K solution. Three complementary techniques, electrochemistry, zetametry, and Fourier-transform infrared spectrometry, were used to investigate pH and ionic strength effects on a MIP’s design and the further recognition process of the analytes by the imprints. Several MIPs were thus designed in acidic, neutral, and basic media and at various ionic strength values. Results indicate that the most appropriate conditions, to achieve a successful MIPs, were an ionic strength of 167 mM and a pH of 7.4. Sensitivity and dissociation constant of the designed sensor were of order of (3.36 ± 0.13) µA·cm−2·mg−1·mL and (8.56 ± 6.09) × 10−11 mg/mL, respectively.

Application of CRISPR Tools for Variant Interpretation and Disease Modeling in Inherited Retinal Dystrophies

Inherited retinal dystrophies are an assorted group of rare diseases that collectively account for the major cause of visual impairment of genetic origin worldwide. Besides clinically, these vision loss disorders present a high genetic and allelic heterogeneity. To date, over 250 genes have been associated to retinal dystrophies with reported causative variants of every nature (nonsense, missense, frameshift, splice-site, large rearrangements, and so forth). Except for a fistful of mutations, most of them are private and affect one or few families, making it a challenge to ratify the newly identified candidate genes or the pathogenicity of dubious variants in disease-associated loci. A recurrent option involves altering the gene in in vitro or in vivo systems to contrast the resulting phenotype and molecular imprint. To validate specific mutations, the process must rely on simulating the precise genetic change, which, until recently, proved to be a difficult endeavor. The rise of the CRISPR/Cas9 technology and its adaptation for genetic engineering now offers a resourceful suite of tools to alleviate the process of functional studies. Here we review the implementation of these RNA-programmable Cas9 nucleases in culture-based and animal models to elucidate the role of novel genes and variants in retinal dystrophies.