NeuralBeds: Neural embeddings for efficient DNA data compression and optimized similarity search.

The availability of high throughput sequencing tools coupled with the declining costs in the production of DNA sequences has led to the generation of enormous amounts of omics data curated in several databases such as NCBI and EMBL. Identification of similar DNA sequences from these databases is one of the fundamental tasks in bioinformatics. It is essential for discovering homologous sequences in organisms, phylogenetic studies of evolutionary relationships among several biological entities, or detection of pathogens. Improving DNA similarity search is of outmost importance because of the increased complexity of the evergrowing repositories of sequences. Therefore, instead of using the conventional approach of comparing raw sequences, e.g., in fasta format, a numerical representation of the sequences can be used to calculate their similarities and optimize the search process. In this study, we analyzed different approaches for numerical embeddings, including Chaos Game Representation, hashing, and neural networks, and compared them with classical approaches such as principal component analysis. It turned out that neural networks generate embeddings that are able to capture the similarity between DNA sequences as a distance measure and outperform the other approaches on DNA similarity search, significantly.

Solubilization and extraction of curcumin from Curcuma Longa using green, sustainable, and food-approved surfactant-free microemulsions.

Curcumin is a powerful coloring agent widely used in the food industry. Its extraction from the plant Curcuma longa is commonly done with aqueous solvent solutions. In contrast to the conventional extraction methods, the present study aimed to compare two different green and bio-based surfactant-free microemulsion (SFME) extraction systems, which are approved for food and yield a higher extracting power of curcuminoids. Two SFMEs, water/ethanol/triacetin and water/diacetin/triacetin, were investigated via dynamic light scattering. Curcumin solubility in binary mixtures consisting of ethanol/triacetin or diacetin/triacetin was studied both experimentally and theoretically using UV-Vis measurements and COSMO-RS. The SFMEs were further examined and compared to a common ethanol/water (80/20) extraction mixture with respect to their extracting ability using high performance liquid chromatography. The SFMEs containing ethanol were found to extract ~18% more curcuminoids than the SFMEs containing diacetin and ~53% more than the ordinary ethanol/water mixture.

Shedding Light on the Diversity of Surfactant Interactions with Luminol Electrochemiluminescence for Bioanalysis.

Luminol is a major probe for chemiluminescence (CL) and electrochemiluminescence (ECL) detection technologies in (bio)analysis. Surfactants are added to ECL assay cocktails to enhance signals or are present, owing to given bioassay protocols, yet little is known regarding their effects on luminol ECL. In-depth understanding is provided here through a broad study with bioanalytically relevant surfactants (cationic, anionic, and nonionic), four common electrode materials, and two luminol derivatives. Naturally, in ECL, surface effects are dominant; however, bulk solution, diffusion, and luminescence-stabilization processes also contribute significantly to the overall reaction. It was found that in contrast to CL the effect surfactants have on luminol ECL cannot be linked to general surfactant characteristics such as ionic nature, hydrophilic lipophilic balance (HLB) value, and critical micellar concentration (CMC). Instead, surfactants act in an all-encompassing mechanism, including surface electrochemistry, their solution and interfacial phases, and the chemical luminescence pathway. This leads to dramatic differences in signals obtained, ranging from 5-fold increases to total quenching. Within this complexity, we defined six guiding principles that are extrapolated from the underlying mechanisms and selection guides for surfactant, electrode, and environmental condition combinations. Those will now assist in developing highly sensitive luminol-ECL-based bioassays, because the surfactant selection can be based not only on properties needed for the assay protocol but also on identifying the optimal electrode-surfactant pair to maximize detection efficiency.

Ab initio prediction of structuring/mesoscale inhomogeneities in surfactant-free microemulsions and hydrogen-bonding-free microemulsions.

In this paper, we consider the influence of H-bond donor and acceptor functionalities on the formation of mesoscale inhomogeneities in ternary systems. It was found that hydrogen-bonding re-enforces such structures, but is not necessarily a prerequisite for the occurrence of mesoscale, microemulsion-like structuring in ternary surfactant-free microemulsions (SFME) and consequently, hydrogen-bonding-free microemulsions (HBFME) exist. The evaluated ternary systems were investigated by means of dynamic light scattering (DLS) and computer-based calculation methods. Theoretical COSMO-RS based calculations were applied to provide an explanation for different hydrotropic efficiencies, and COSMOplex calculations were used to predict and evaluate the propensity of the molecules to form mesoscale structures in SFME and HBFME. Microemulsion-like fluctuations could be observed in the COSMOplex simulations and correlate fairly well with the appearance of mesoscopic structures observed in SFME and HBFME, although the free energy differences in the formation of aggregate structures in the investigated systems are very small, in the range of 0.05 kcal mol-1.

Role of Amine Functionality for CO2 Chemisorption on Silica.

The mechanism of CO2 adsorption on primary, secondary, and bibasic aminosilanes synthetically functionalized in porous SiO2 was qualitatively and quantitatively investigated by a combination of IR spectroscopy, thermogravimetry, and quantum mechanical modeling. The mode of CO2 adsorption depends particularly on the nature of the amine group and the spacing between the aminosilanes. Primary amines bonded CO2 preferentially through the formation of intermolecular ammonium carbamates, whereas CO2 was predominantly stabilized as carbamic acid, when interacting with secondary amines. Ammonium carbamate formation requires the transfer of the carbamic acid proton to a second primary amine group to form the ammonium ion and hence two (primary) amine groups are required to bind one CO2 molecule. The higher base strength of secondary amines enables the stabilization of carbamic acid, which is thereby hindered to interact further with nearby amine functions, because their association with Si-OH groups (either protonation or hydrogen bonding) does not allow further stabilization of carbamic acid as carbamate. Steric hindrance of the formation of intermolecular ammonium carbamates leads to higher uptake capacities for secondary amines functionalized in porous SiO2 at higher amine densities. In aminosilanes possessing a primary and a secondary amine group, the secondary amine group tends to be protonated by Si-OH groups and therefore does not substantially interact with CO2.

Stability of amorphous silica-alumina in hot liquid water.

Herein, the hydrothermal stability of amorphous silica-alumina (ASA) is investigated under conditions relevant for the catalytic conversion of biomass, namely in liquid water at 200 °C. The hydrothermal stability of ASA is much higher than that of pure silica or alumina. Interestingly, the synthetic procedure used plays a major role in its resultant stability: ASA prepared by cogelation (CG) lost its microporous structure, owing to hydrolysis of the siloxane bonds, but the resulting mesoporous material still had a considerable surface area. ASA prepared by deposition precipitation (DP) contained a silicon-rich core and an aluminum-rich shell. In hot liquid water, the latter structure was transformed into a layer of amorphous boehmite, which protected the particle from further hydrolysis. The surface area showed relatively minor changes during the transformation. Independent of the synthetic method used, the ASAs retained a considerable concentration of acid sites. The concentration of acid sites qualitatively followed the changes in surface area, but the changes were less pronounced. The performance of different ASAs for the hydrolysis of cellobiose into glucose is compared.