Hydrodynamic and Polyelectrolyte Properties of Actin Filaments: Theory and Experiments

Actin filament′s polyelectrolyte and hydrodynamic properties, their interactions with the biological environment, and external force fields play an essential role in their biological activities in eukaryotic cellular processes. In this article, we introduce a unique approach that combines dynamics and electrophoresis light scattering experiments, an extended semiflexible worm-like chain model, and an asymmetric polymer length distribution theory to characterize the polyelectrolyte and hydrodynamic properties of actin filaments in aqueous electrolyte solutions. We used the same sample and experimental conditions and considered several g-actin and polymerization buffers to elucidate the impact of their chemical composition, reducing agents, pH values, and ionic strengths on the filament translational diffusion coefficient, electrophoretic mobility, structure factor, asymmetric length distribution, effective filament diameter, electric charge, zeta potential, and semiflexibility. Compared to those values obtained from molecular structure models, our results revealed a lower value of the effective G-actin charge and a more significant value of the effective filament diameter due to the formation of the double layer of the electrolyte surrounding the filaments. Additionally, compared to the values usually reported from electron micrographs, the lower values of our results for the persistence length and average contour filament length agrees with the significant difference in the association rates at the filament ends that shift to submicro lengths, the maximum of the length distribution.

Phylogenetic signal in characters from Aristotle’s History of Animals

The influential Greek philosopher Aristotle (384-322 BCE) is almost unanimously acclaimed as the founder of zoology. There is a consensus that he was interested in attributes of animals, but whether or not he tried to develop a zoological taxonomy remains controversial. Fürst von Lieven and Humar compiled a data matrix from Aristotle’s Historia animalium and showed, through a parsimony analysis published in 2008, that these data produced a hierarchy that matched several taxa recognized by Aristotle. However, their analysis leaves some questions unanswered because random data can sometimes yield fairly resolved trees. In this study, we update the scores of many cells and add four new characters to the data matrix (147 taxa scored for 161 characters) and quote passages from Aristotle’s Historia animalium to justify these changes. We confirm the presence of a phylogenetic signal in these data through a test using skewness in length distribution of a million random trees, which shows that many of the characters discussed by Aristotle were systematically relevant. Our parsimony analyses on the updated matrix recover far more trees than reported by Fürst von Lieven and Humar, but their consensus includes many taxa that Aristotle recognized and apparently named for the first time, such as selachē (selachians) and dithyra (Bivalvia Linnaeus, 1758). This study suggests that even though taxonomy was obviously not Aristotle’s chief interest in Historia animalium, it was probably among his secondary interests. These results may pave the way for further taxonomic studies in Aristotle’s zoological writings in general. Despite being almost peripheral to Aristotle’s writings, his taxonomic contributions are clearly major achievements.

Freight Distribution Analysis and Modelling of Inland Waterway Transport along the Yangtze River Economic Belt using Big Data

The Yangtze River Economic Belt (YREB) serves as the main east-west axis of China to promote economic development and environmental protection along the Yangtze River. This paper analyses the factors that affect the freight distribution of major types of cargo transported through the Yangtze River, using data from the automatic identification system (AIS) and ship visa data. First, a set of freight impedance functions are developed for different types of links of the waterway network, by considering a number of factors such as cargo types, delays at ship locks, water levels and flows at different waterway segments and upstream and downstream shipping speeds. Both the distance- and time-based impedance matrices of different types of cargo are computed, respectively. After that, gravity model (GM) and intervening opportunity model (IOM) are estimated to simulate the distribution of different types of cargo based on the computed impedance matrices. Meanwhile, a trip length distribution (TLD) method is applied to validate the estimated distribution models. The results indicate that GM with a power term outperforms other models, and the time-based models are superior to the distance-based ones for the prediction of freight distributions over large geographies like the YREB. This work offers an in-depth understanding of the freight characteristics of inland waterways and therefore it should be helpful for relevant authorities in formulating their port and inland waterway plans and policies.

Analysis of the Parameters Affecting the Stiffness of Short Sisal Fiber Biocomposites Manufactured by Compression-Molding

The use of natural fiber-based composites is on the rise in many industries. Thanks to their eco-sustainability, these innovative materials make it possible to adapt the production of components, systems and machines to the increasingly stringent regulations on environmental protection, while at the same time reducing production costs, weight and operating costs. Optimizing the mechanical properties of biocomposites is an important goal of applied research. In this work, using a new numerical approach, the effects of the volume fraction, average length, distribution of orientation and curvature of fibers on the Young’s modulus of a biocomposite reinforced with short natural fibers were studied. Although the proposed approach could be applied to any biocomposite, sisal fibers and an eco-sustainable thermosetting matrix (green epoxy) were considered in both simulations and the associated experimental assessment. The results of the simulations showed the following effects of the aforementioned parameters on Young’s modulus: a linear growth with the volume fraction, nonlinear growth as the length of the fibers increased, a reduction as the average curvature increased and an increase in stiffness in the x-y plane as the distribution of fiber orientation in the z direction decreased.

Deconvolution of fission-track length distributions and its application to dating and separating pre- and post-depositional components

To enable the separation of pre- and postdepositional components of the length distribution of (partially annealed) horizontal confined fission tracks, the length distribution is corrected by deconvolution. Probabilistic least-squares inversion corrects natural track length histograms for observational biases, considering the variance in data, modelization, and prior information. The corrected histogram is validated by its variance–covariance matrix. It is considered that horizontal track data can exist with or without measurements of angles to the c axis. In the latter case, 3D histograms are introduced as an alternative to histograms of c-axis-projected track lengths. Thermal history modelling of samples is not necessary for the calculation of track age distributions of corrected tracks. In an example, the age equations are applied to apatites with predepositional (inherited) tracks in order to extract the postdepositional track length histogram. Fission tracks generated before deposition in detrital apatite crystals are mixed with post-depositional tracks. This complicates the calculation of the post-sedimentary thermal history, as the grains have experienced different thermal histories prior to deposition. Thereafter, the grains share a common thermal history. Thus, the extracted post-depositional histogram without inherited tracks may be used for thermal history calculation.

Reactive Crystallization Kinetics of K2SO4 from Picromerite-Based MgSO4 and KCl

In this work, the kinetic parameters, the degrees of initial supersaturation (S0) and the profiles of supersaturation (S) were determined for the reactive crystallization of K2SO4 from picromerite (K2SO4.MgSO4.6H2O) and KCl. Different reaction temperatures between 5 and 45 °C were considered, and several process analytical techniques were applied. Along with the solution temperature, the crystal chord length distribution (CLD) was continuously followed by an FBRM probe, images of nucleation and growth events as well as the crystal morphology were captured, and the absorbance of the solution was measured via ATR-FTIR spectroscopy. In addition, the ion concentrations were analyzed. It was found that S0 is inversely proportional to the reactive crystallization temperature in the K+, Mg2+/Cl−, SO42−//H2O system at 25 °C, where S0 promotes nucleation and crystal growth of K2SO4 leading to a bimodal CLD. The CLD was converted to square-weighted chord lengths for each S0 to determine the secondary nucleation rate (B), crystal growth rate (G), and suspension density (MT). By correlation, from primary nucleation rate (Bb) and G with S0, the empirical parameters b = 3.61 and g = 4.61 were obtained as the order of primary nucleation and growth, respectively. B versus G and MT were correlated to the reaction temperature providing the rate constants of B and respective activation energy, E = 69.83 kJ∙mol−1. Finally, a general Equation was derived that describes B with parameters KR = 13,810.8, i = 0.75 and j = 0.71. The K2SO4 crystals produced were of high purity, containing maximal 0.51 wt% Mg impurity, and were received with ~73% yield at 5 °C.

The Physicochemical Properties of Starch Are Affected by Wxlv in Indica Rice

Amylose largely determines rice grain quality profiles. The process of rice amylose biosynthesis is mainly driven by the waxy (Wx) gene, which also affects the diversity of amylose content. The present study assessed the grain quality profiles, starch fine structure, and crystallinity characteristics of the near-isogenic lines Q11(Wxlv), NIL(Wxa), and NIL(Wxb) in the indica rice Q11 background containing different Wx alleles. Q11(Wxlv) rice contained a relatively higher amylose level but very soft gel consistency and low starch viscosity, compared with rice lines carrying Wxa and Wxb. In addition, starch fine structure analysis revealed a remarkable decrease in the relative area ratio of the short amylopectin fraction but an increased amylose fraction in Q11(Wxlv) rice. Chain length distribution analysis showed that Q11(Wxlv) rice contained less amylopectin short chains but more intermediate chains, which decreased the crystallinity and lamellar peak intensity, compared with those of NIL(Wxa) and NIL(Wxb) rice. Additionally, the starches in developing grains showed different accumulation profiles among the three rice lines. Moreover, significant differences in starch gelatinization and retrogradation characteristics were observed between near-isogenic lines, which were caused by variation in starch fine structure. These findings revealed the effects of Wxlv on rice grain quality and the fine structure of starch in indica rice.

The Design and Implementation of an Improved Lightweight BLASTP on CUDA GPU

In the field of computational biology, sequence alignment is a very important methodology. BLAST is a very common tool for performing sequence alignment in bioinformatics provided by National Center for Biotechnology Information (NCBI) in the USA. The BLAST server receives tens of thousands of queries every day on average. Among the procedures of BLAST, the hit detection process whose core architecture is a lookup table is the most time-consuming. In the latest work, a lightweight BLASTP on CUDA GPU with a hybrid query-index table was proposed for servicing the sequence query length shorter than 512, which effectively improved the query efficiency. According to the reported protein sequence length distribution, about 90% of sequences are equal to or smaller than 1024. In this paper, we propose an improved lightweight BLASTP to speed up the hit detection time for longer query sequences. The largest sequence is enlarged from 512 to 1024. As a result, one more bit is required to encode each sequence position. To meet the requirement, an extended hybrid query-index table (EHQIT) is proposed to accommodate three sequence positions in a four-byte table entry, making only one memory access sufficient to retrieve all the position information as long as the number of hits is equal to or smaller than three. Moreover, if there are more than three hits for a possible word, all the position information will be stored in contiguous table entries, which eliminates branch divergence and reduces memory space for pointers to overflow buffer. A square symmetric scoring matrix, Blosum62, is used to determine the relative score made by matching two characters in a sequence alignment. The experimental results show that for queries shorter than 512 our improved lightweight BLASTP outperforms the original lightweight BLASTP with speedups of 1.2 on average. When the number of hit overflows increases, the speedup can be as high as two. For queries shorter than 1024, our improved lightweight BLASTP can provide speedups ranging from 1.56 to 3.08 over the CUDA-BLAST. In short, the improved lightweight BLASTP can replace the original one because it can support a longer query sequence and provide better performance.

Enzymatic Hydrolysis of Broken Rice Protein: Antioxidant Activities by Chemical and Cellular Antioxidant Methods

Excessive reactive oxygen species (ROS) is an important cause of aging, and supplementing antioxidants through diet is one of the important ways to delay aging. Some studies have confirmed that rice protease hydrolysate has antioxidant activity, but was rarely been investigated on cells. Thus, commercial enzymes, alkaline enzyme, neutral enzyme, pepsin, chymotrypsin, and trypsin were selected to hydrolyze broken rice protein (BRP) to obtain the corresponding hydrolysates, which were A-broken rice protein hydrolysate (BRPH), N-BRPH, P-BRPH, C-BRPH, and T-BRPH, respectively. Then the antioxidant properties of BRPHs were evaluated by different chemical and cellular antioxidation. Molecular weight, peptide length distribution, and amino acid sequence were detected to insight into the antioxidant properties. Among BRPHs, the A-BRPH displayed the strongest hydroxyl radical scavenging activity (IC50 = 1.159 mg/ml) and metal ion-chelating activities (IC50 = 0.391 mg/ml). Furthermore, cellular antioxidation confirmed that A-BRPH significantly increased cell viability and inhibited the intracellular ROS release in both aging cells and cell-aging processes. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) results revealed that peptides with molecular weight <14.5 KDa were produced by enzymatic hydrolysis. Additionally, A-BRPH rich in low molecular weight (<3 kDa) and short-length peptides with some specific amino acids, such as aromatic and hydrophobic amino acids, contributes to the antioxidant properties. This study provided theoretical to the utilization of broken rice and confirmed that A-BRPH could be used in new anti-aging food and health products for human consumption.