Recursive MAGUS: Scalable and accurate multiple sequence alignment

Multiple sequence alignment tools struggle to keep pace with rapidly growing sequence data, as few methods can handle large datasets while maintaining alignment accuracy. We recently introduced MAGUS, a new state-of-the-art method for aligning large numbers of sequences. In this paper, we present a comprehensive set of enhancements that allow MAGUS to align vastly larger datasets with greater speed. We compare MAGUS to other leading alignment methods on datasets of up to one million sequences. Our results demonstrate the advantages of MAGUS over other alignment software in both accuracy and speed. MAGUS is freely available in open-source form at https://github.com/vlasmirnov/MAGUS.     

Switching of membrane organelles between cytoskeletal transport systems is determined by regulation of the microtubule-based transport

Intracellular transport of membrane organelles occurs along microtubules (MTs) and actin filaments (AFs). Although transport along each type of the cytoskeletal tracks is well characterized, the switching between the two types of transport is poorly understood because it cannot be observed directly in living cells. To gain insight into the regulation of the switching of membrane organelles between the two major transport systems, we developed a novel approach that combines live cell imaging with computational modeling. Using this approach, we measured the parameters that determine how fast membrane organelles switch back and forth between MTs and AFs (the switching rate constants) and compared these parameters during different signaling states. We show that regulation involves a major change in a single parameter: the transferring rate from AFs onto MTs. This result suggests that MT transport is the defining factor whose regulation determines the choice of the cytoskeletal tracks during the transport of membrane organelles.     

Measurement,model prediction and uncertainty quantification of plasma clearance of cerium citrate in humans

Radiation and Environmental Biophysics - Double tracer studies in healthy human volunteers with stable isotopes of cerium citrate were performed with the aim of investigating the gastro-intestinal...     

Very-Long-Chain Wax Constituents from Primula veris and P. acaulis: Does the Paradigm of Non-Branched vs. Branched Chain Dominance Universally Hold in all Plant Taxa?

Herein n-, iso- and anteiso-series of very-long-chained (VLC) alkanes (C₂₁–C₃₅), fatty acid benzyl esters (FABEs; C₂₀–C₃₂), and 2-alkanones (C₂₃–C₃₅) were identified in the wax of Primula veris L. and P. acaulis (L.) L. (Primulaceae). For the very first time in a sample of natural origin, the presence of iso- and anteiso-VLC FABEs and 2-alkanones was unequivocally confirmed by synthetic work, derivatization, and NMR. It should be noted that the studied species produced unusually high amounts of branched wax constituents (e. g., >50 % of 2-alkanones were branched isomers). The domination of iso-isomers, probably biosynthesized from leucine-derived starters, is a unique feature in the Plant Kingdom. The plant organ distribution of these VLC compounds in P. acaulis samples (different habitats and phenological phases) pointed to their possible ecological value. This was supported by a eutectic behavior of binary blends of FABEs and alkanes, as well as by high UV-C absorption by FABEs.     

Pretreatment of sugarcane bagasse using supercritical carbon dioxide combined with ultrasound to improve the enzymatic hydrolysis

This work evaluates the pretreatment of sugarcane bagasse combining supercritical carbon dioxide (SC-CO₂) and ultrasound to enhance the enzymatic hydrolysis of pretreated bagasse. In a first step the influence of process variables on the SC-CO₂ pretreatment to enhance the enzymatic hydrolysis was evaluated by mean of a Plackett–Burmann design. Then, the sequential treatment combining ultrasound + SC-CO₂ was evaluated. Results show that treatment using SC-CO₂ increased the amount of fermentable sugar obtained of about 280% compared with the non-treated bagasse, leading to a hydrolysis efficiency (based on the amount of cellulose) as high as 74.2%. Combining ultrasound + SC-CO₂ treatment increased about 16% the amount of fermentable sugar obtained by enzymatic hydrolysis in comparison with the treatment using only ultrasound. From the results presented in this work it can be concluded that the combined ultrasound + SC-CO₂ treatment is an efficient and promising alternative to carry out the pretreatment of lignocellulosic feedstock at relatively low temperatures without the use of hazardous solvents.     

Platinum(II) complexes with steroidal esters of L-methionine and L-histidine: synthesis, characterization and cytotoxic activity

Twelve steroidal platinum(II) complexes were synthesized by reaction of potassium tetrachloroplatinate with steroidal esters of L-methionine and L-histidine. The steroidal esters coordinated as bidentate ligands via S and N donor atoms of L-methionine and via two N donor atoms of L-histidine. Cholesterol, cholestanol, diosgenine, pregnenolone, dehydroepiandrosterone, testosterone, estrone, and estradiol were used as the steroidal compounds. The esters and complexes prepared were characterized by infrared, mass, and (1)H NMR spectroscopy and elemental analysis. Platinum complexes were tested for in vitro cytotoxicity against several cancer cell lines: T-lymphoblastic leukemia CEM, breast carcinoma MCF-7, lung carcinoma A-549, multiple myeloma RPMI 8226, and one normal cell line human fibroblast BJ.