Survey of Heterodera glycines population abundance and virulence phenotypes during 2021-2022 in Heilongjiang Province.

Soybean cyst nematode (SCN), Heterodera glycines, poses a significant threat to global soybean production. Heilongjiang, the largest soybean-producing province in China, contributes over 40% to the country's total yield. This province has much longer history of SCN infestation. To assess the current situation in Heilongjiang, we conducted a survey to determine the SCN population density and virulence phenotypes during 2021-2022 and compared the data with a previous study in 2015. A total of 377 soil samples from 48 counties representing eleven major soybean-planting regions were collected. The prevalence of SCN increased from 55.4% in 2015 to 59% in the current survey. The population densities ranged from 80 to 26,700 eggs and juveniles per 100 cm3 of soil. Virulence phenotypes were evaluated for 60 representative SCN populations using the HG type test, revealing nine different HG types. The most common virulence phenotypes were HG types 7 and 0, accounting for 56.7% and 20% of all SCN populations, respectively. The prevalence of populations with a reproductive index (FI) greater than 10% on PI548316 increased from 64.5% in 2015 to 71.7%. However, the FI on the commonly used resistance sources PI 548402 (Peking) and PI 437654 remained low at 3.3%. These findings highlight the increasing prevalence and changing virulence phenotypes of SCN in Heilongjiang. They also emphasize the importance of rotating soybean varieties with different resistance sources and urgently identifying new sources of resistance to combat SCN.

Combined Detection of IFN-γ and Lymphocyte Subsets with Activation Indicators in the Clinical Application of Mycobacterium Tuberculosis Infection at Different Times.

The immune status of mycobacterium tuberculosis (MTB) infection is essential for the diagnosis and treatment of this disease. In this work, we aim to evaluate the clinical significance of the combination of serum IFN-γ, IGRAs (Interferon-Gamma Release Assay), lymphocyte subset with activation indicators detection in active and latent tuberculosis infection patients. For this study, anticoagulant whole blood were collected from 45 active tuberculosis (AT group), 44 latent tuberculosis (LT group) and 32 healthy controls (HCs group). The serum IFN-γ and IGRAs detected by chemiluminescence, and the percentage of lymphocyte subsets and activated lymphocytes detected by flow cytometry. The results showed combined IGRAs, serum IFN-γ and NKT cells not only has good diagnostic efficiency for the AT, but also provides a laboratory diagnostic method to distinguish AT from LT. Activation indicator of CD3+HLA-DR+T and CD4+HLA-DR+T can effectively distinguish LT from HCs. While combined CD3+T, CD4+T, CD8+CD28+T, Treg and CD16+CD56+CD69+ cells can distinguish AT from HCs. This study showed combined direct detection of serum IFN-γ and IGRAs as well as lymphocyte subsets with activation indicators which may provide laboratory basis for the diagnosis and differential diagnosis of active and latent MTB infection.

Chemical Reaction Networks' Programming for Solving Equations.

The computational ability of the chemical reaction networks (CRNs) using DNA as the substrate has been verified previously. To solve more complex computational problems and perform the computational steps as expected, the practical design of the basic modules of calculation and the steps in the reactions have become the basic requirements for biomolecular computing. This paper presents a method for solving nonlinear equations in the CRNs with DNA as the substrate. We used the basic calculation module of the CRNs with a gateless structure to design discrete and analog algorithms and realized the nonlinear equations that could not be solved in the previous work, such as exponential, logarithmic, and simple triangle equations. The solution of the equation uses the transformation method, Taylor expansion, and Newton iteration method, and the simulation verified this through examples. We used and improved the basic calculation module of the CRN++ programming language, optimized the error in the basic module, and analyzed the error's variation over time.

Allosteric DNAzyme-based DNA logic circuit: operations and dynamic analysis.

Recently, due to the dual roles of DNA and enzyme, DNAzyme has been widely used in the field of DNA circuit, which has a wide range of applications in bio-engineered system, information processing and biocomputing. In fact, the activity of DNAzymes was regulated by subunits assembly, pH control and metal ions triggers. However, those regulations required to change the sequences of whole DNAzyme, as separating parts and inserting extra DNA sequence. Inspired by the allosteric regulation of proteins in nature, a new allosteric strategy is proposed to regulate the activity of DNAzyme without DNA sequences changes. In this strategy, DNA strand displacement was used to regulate the DNAzyme structure, through which the activity of DNAzyme was well controlled. The strategy was applied to E6-type DNAzymes, and the operations of DNA logic circuit (YES, OR, AND, cascading and feedback) were established and simulated with the dynamic analyses. The allosteric regulation has potential to construct more complicated molecular systems, which can be applied to bio-sensing and detection.

Constructing Controllable Logic Circuits Based on DNAzyme Activity.

Recently, DNA molecules have been widely used to construct advanced logic devices due to their unique properties, such as a simple structure and predictable behavior. In fact, there are still many challenges in the process of building logic circuits. Among them, the scalability of the logic circuit and the elimination of the crosstalk of the cascade circuit have become the focus of research. Inspired by biological allosteric regulation, we developed a controllable molecular logic circuit strategy based on the activity of DNAzyme. The E6 DNAzyme sequence was temporarily blocked by hairpin DNA and activated under appropriate input trigger conditions. Using a substrate with ribonucleobase (rA) modification as the detection strand, a series of binary basic logic gates (YES, AND, and INHIBIT) were implemented on the computational component platform. At the same time, we demonstrate a parallel demultiplexer and two multi-level cascade circuits (YES-YES and YES-Three input AND (YES-TAND)). In addition, the leakage of the cascade process was reduced by exploring factors such as concentration and DNA structure. The proposed DNAzyme activity regulation strategy provides great potential for the expansion of logic circuits in the future.

8-Bit Adder and Subtractor with Domain Label Based on DNA Strand Displacement.

DNA strand displacement, which plays a fundamental role in DNA computing, has been widely applied to many biological computing problems, including biological logic circuits. However, there are many biological cascade logic circuits with domain labels based on DNA strand displacement that have not yet been designed. Thus, in this paper, cascade 8-bit adder/subtractor with a domain label is designed based on DNA strand displacement; domain t and domain f represent signal 1 and signal 0, respectively, instead of domain t and domain f are applied to representing signal 1 and signal 0 respectively instead of high concentration and low concentration high concentration and low concentration. Basic logic gates, an amplification gate, a fan-out gate and a reporter gate are correspondingly reconstructed as domain label gates. The simulation results of Visual DSD show the feasibility and accuracy of the logic calculation model of the adder/subtractor designed in this paper. It is a useful exploration that may expand the application of the molecular logic circuit.

Correcting Errors in Image Encryption Based on DNA Coding.

As a primary method, image encryption is widely used to protect the security of image information. In recent years, image encryption pays attention to the combination with DNA computing. In this work, we propose a novel method to correct errors in image encryption, which results from the uncertainty of DNA computing. DNA coding is the key step for DNA computing that could decrease the similarity of DNA sequences in DNA computing as well as correct errors from the process of image encryption and decryption. The experimental results show our method could be used to correct errors in image encryption based on DNA coding.

Genetic diversity and genetic relationships of japonica rice varieties in Northeast Asia based on SSR markers.

Genetic diversity and the relationship among nine japonica rice groups consisting of 288 landraces and varieties in different geographical origins of Northeast Asia (China, Japan, Korea, Democratic People's Republic of Korea) and the Russian Far East district of the Russian Federation were evaluated with 154 simple sequence repeat (SSR) markers. A total of 823 alleles were detected. The observed allele numbers (Na) per locus, Nei's gene diversity (He) and the polymorphism information content (PIC) ranged from 2 to 9, 0.061 to 0.869 and 0.060 to 0.856, with an average of 5.344, 0.624 and 0.586, respectively. Five SSR loci, RM1350, RM1369, RM257, RM336 and RM1374, provided the highest PIC values and are potential for exploring the genetic diversity of rice cultivars in Northeast Asia. Molecular variance analysis showed that a significant difference existed both among groups (91.6%) and within each group (8.4%). The low genetic variation within each group indicated that the gene pool is narrow and alien genetic variation should be introduced into the rice breeding program in Northeast Asia. Based on the He and PIC values, the nine groups were ranked in a descending order: Heilongjiang landraces, Jilin landraces, Japanese improved varieties, Heilongjiang improved varieties, Russian Far East district of the Russian Federation improved varieties, Liaoning improved varieties, Jilin improved varieties, Korean improved varieties and Democratic People's Republic of Korea improved varieties. The nine groups were further divided into three subgroups and the 288 varieties into five clusters. This study provided information for parent selection in order to broaden the gene pool of the japonica rice germplasm in Northeast Asia.

DNA Sequences Under Multiple Guanine-Cytosine (GC) Base Pairs Constraint.

DNA computing is a new computing method that has high efficiency in solving large-scale nonlinear and Non-deterministic Polynomial complete problems. The design of DNA sequences is an important step in DNA computing, and the quality of the DNA sequences directly affects the accuracy of DNA computing results. Efficiently designing high-quality DNA sequences is currently a significant challenge. In order to improve the efficiency of DNA sequence design, a sparrow evolutionary search algorithm (SESA) is proposed by us. It inherits the fast convergence of the sparrow search algorithm and avoids the situation that the sparrow search algorithm is prone to fall into a local optimum, which greatly improves the search performance of the algorithm on discrete numerical problems. In order to improve the quality of DNA sequence, a new constraint, multiple GC constraint, has been proposed in this paper. Simulated experiments in NUPACK show that this constraint can greatly improve the quality of the DNA sequences designed by us. Compared with previous results, our DNA sequences have better stability.

H-ACO with Consecutive Bases Pairing Constraint for Designing DNA Sequences.

DNA computing is a novel computing method that does not rely on traditional computers. The design of DNA sequences is a crucial step in DNA computing, and the quality of the sequence design directly affects the results of DNA computing. In this paper, a new constraint called the consecutive base pairing constraint is proposed to limit specific base pairings in DNA sequence design. Additionally, to improve the efficiency and capability of DNA sequence design, the Hierarchy-ant colony (H-ACO) algorithm is introduced, which combines the features of multiple algorithms and optimizes discrete numerical calculations. Experimental results show that the H-ACO algorithm performs well in DNA sequence design. Finally, this paper compares a series of constraint values and NUPACK simulation data with previous design results, and the DNA sequence set designed in this paper has more advantages.

Freeze-Thaw Cycle Durability and Mechanism Analysis of Zeolite Powder-Modified Recycled Concrete.

The inferior mechanical performance and freeze-thaw (FT) resistance of recycled concrete are mostly due to the significant water absorption and porosity of recycled coarse particles. In this study, different dosages of zeolite powder were used in recycled concrete. A series of macroscopic tests were used to evaluate the workability and FT durability of zeolite powder-modified recycled concrete (ZPRC). X-ray diffraction (XRD) and scanning electron microscopy (SEM) were used to reveal the micro-mechanisms of FT resistance in ZPRC. The results show that the increase in zeolite powder content leads to a decrease in the slump and water absorption of ZPRC. Additionally, ZPRC with 10% zeolite powder has superior mechanical characteristics and tolerance to FT conditions. The higher strength and FT resistance of the ZPRC can be attributed to the particle-filling effect, water storage function, and pozzolanic reaction of zeolite powder, which results in a denser microstructure. The particle-filling effect of zeolite powder promotes the reduction of surface pores in recycled coarse aggregates (RCAs). The water storage function of zeolite powder can provide water for the secondary hydration of cement particles while reducing the free water content in ZPRC. The pozzolanic reaction of zeolite powder can also promote the generation of hydrated calcium silicate and anorthite, thereby making the microstructure of ZPRC more compact. These results provide theoretical guidance for the engineering application of recycled concrete in cold regions.

Integrated improved Harris hawks optimization for global and engineering optimization.

The original Harris hawks optimization (HHO) algorithm has the problems of unstable optimization effect and easy to fall into stagnation. However, most of the improved HHO algorithms can not effectively improve the ability of the algorithm to jump out of the local optimum. In this regard, an integrated improved HHO (IIHHO) algorithm is proposed. Firstly, the linear transformation escape energy used by the original HHO algorithm is relatively simple and lacks the escape law of the prey in the actual nature. Therefore, intermittent energy regulator is introduced to adjust the energy of Harris hawks, which is conducive to improving the local search ability of the algorithm while restoring the prey's rest mechanism; Secondly, to adjust the uncertainty of random vector, a more regular vector change mechanism is used instead, and the attenuation vector is obtained by modifying the composite function. Finally, the search scope of Levy flight is further clarified, which is conducive to the algorithm jumping out of the local optimum. Finally, in order to modify the calculation limitations caused by the fixed step size, Cardano formula function is introduced to adjust the step size setting and improve the accuracy of the algorithm. First, the performance of IIHHO algorithm is analyzed on the Computational Experimental Competition 2013 (CEC 2013) function test set and compared with seven improved evolutionary algorithms, and the convergence value of the iterative curve obtained is better than most of the improved algorithms, verifying the effectiveness of the proposed IIHHO algorithm. Second, the IIHHO is compared with another three state of the art (SOTA) algorithms with the Computational Experimental Competition 2022 (CEC 2022) function test set, the experiments show that the proposed IIHHO algorithm still has a strong ability to search for the optimal value. Third, IIHHO algorithm is applied in two different engineering experiments. The calculation results of minimum cost prove that IIHHO algorithm has certain advantages in dealing with the problem of search space. All these demonstrate that the proposed IIHHO is promising for numeric optimization and engineering applications.

Multi-strategy learning-based particle swarm optimization algorithm for COVID-19 threshold segmentation.

With advancements in science and technology, the depth of human research on COVID-19 is increasing, making the investigation of medical images a focal point. Image segmentation, a crucial step preceding image processing, holds significance in the realm of medical image analysis. Traditional threshold image segmentation proves to be less efficient, posing challenges in selecting an appropriate threshold value. In response to these issues, this paper introduces Inner-based multi-strategy particle swarm optimization (IPSOsono) for conducting numerical experiments and enhancing threshold image segmentation in COVID-19 medical images. A novel dynamic oscillatory weight, derived from the PSO variant for single-objective numerical optimization (PSOsono) is incorporated. Simultaneously, the historical optimal positions of individuals in the particle swarm undergo random updates, diminishing the likelihood of algorithm stagnation and local optima. Moreover, an inner selection learning mechanism is proposed in the update of optimal positions, dynamically refining the global optimal solution. In the CEC 2013 benchmark test, PSOsono demonstrates a certain advantage in optimization capability compared to algorithms proposed in recent years, proving the effectiveness and feasibility of PSOsono. In the Minimum Cross Entropy threshold segmentation experiments for COVID-19, PSOsono exhibits a more prominent segmentation capability compared to other algorithms, showing good generalization across 6 CT images and further validating the practicality of the algorithm.

Overexpression of Wild Soybean Expansin Gene GsEXLB14 Enhanced the Tolerance of Transgenic Soybean Hairy Roots to Salt and Drought Stresses.

As a type of cell-wall-relaxing protein that is widely present in plants, expansins have been shown to actively participate in the regulation of plant growth and responses to environmental stress. Wild soybeans have long existed in the wild environment and possess abundant resistance gene resources, which hold significant value for the improvement of cultivated soybean germplasm. In our previous study, we found that the wild soybean expansin gene GsEXLB14 is specifically transcribed in roots, and its transcription level significantly increases under salt and drought stress. To further identify the function of GsEXLB14, in this study, we cloned the CDS sequence of this gene. The transcription pattern of GsEXLB14 in the roots of wild soybean under salt and drought stress was analyzed by qRT-PCR. Using an Agrobacterium rhizogenes-mediated genetic transformation, we obtained soybean hairy roots overexpressing GsEXLB14. Under 150 mM NaCl- and 100 mM mannitol-simulated drought stress, the relative growth values of the number, length, and weight of transgenic soybean hairy roots were significantly higher than those of the control group. We obtained the transcriptomes of transgenic and wild-type soybean hairy roots under normal growth conditions and under salt and drought stress through RNA sequencing. A transcriptomic analysis showed that the transcription of genes encoding expansins (EXPB family), peroxidase, H+-transporting ATPase, and other genes was significantly upregulated in transgenic hairy roots under salt stress. Under drought stress, the transcription of expansin (EXPB/LB family) genes increased in transgenic hairy roots. In addition, the transcription of genes encoding peroxidases, calcium/calmodulin-dependent protein kinases, and dehydration-responsive proteins increased significantly. The results of qRT-PCR also confirmed that the transcription pattern of the above genes was consistent with the transcriptome. The differences in the transcript levels of the above genes may be the potential reason for the strong tolerance of soybean hairy roots overexpressing the GsEXLB14 gene under salt and drought stress. In conclusion, the expansin GsEXLB14 can be used as a valuable candidate gene for the molecular breeding of soybeans.

Multi-omics analysis reveals novel loci and a candidate regulatory gene of unsaturated fatty acids in soybean (Glycine max (L.) Merr).

BACKGROUND: Soybean is a major oil crop; the nutritional components of soybean oil are mainly controlled by unsaturated fatty acids (FA). Unsaturated FAs mainly include oleic acid (OA, 18:1), linoleic acid (LLA, 18:2), and linolenic acid (LNA, 18:3). The genetic architecture of unsaturated FAs in soybean seeds has not been fully elucidated, although many independent studies have been conducted. A 3 V multi-locus random single nucleotide polymorphism (SNP)-effect mixed linear model (3VmrMLM) was established to identify quantitative trait loci (QTLs) and QTL-by-environment interactions (QEIs) for complex traits. RESULTS: In this study, 194 soybean accessions with 36,981 SNPs were calculated using the 3VmrMLM model. As a result, 94 quantitative trait nucleotides (QTNs) and 19 QEIs were detected using single-environment (QTN) and multi-environment (QEI) methods. Three significant QEIs, namely rs4633292, rs39216169, and rs14264702, overlapped with a significant single-environment QTN. CONCLUSIONS: For QTNs and QEIs, further haplotype analysis of candidate genes revealed that the Glyma.03G040400 and Glyma.17G236700 genes were beneficial haplotypes that may be associated with unsaturated FAs. This result provides ideas for the identification of soybean lipid-related genes and provides insights for breeding high oil soybean varieties in the future.

Integrating Genome-Wide Association Study, Transcriptome and Metabolome Reveal Novel QTL and Candidate Genes That Control Protein Content in Soybean.

Protein content (PC) is crucial to the nutritional quality of soybean [Glycine max (L.) Merrill]. In this study, a total of 266 accessions were used to perform a genome-wide association study (GWAS) in three tested environments. A total of 23,131 high-quality SNP markers (MAF ≥ 0.02, missing data ≤ 10%) were identified. A total of 40 association signals were significantly associated with PC. Among them, five novel quantitative trait nucleotides (QTNs) were discovered, and another 32 QTNs were found to be overlapping with the genomic regions of known quantitative trait loci (QTL) related to soybean PC. Combined with GWAS, metabolome and transcriptome sequencing, 59 differentially expressed genes (DEGs) that might control the change in protein content were identified. Meantime, four commonly upregulated differentially abundant metabolites (DAMs) and 29 commonly downregulated DAMs were found. Remarkably, the soybean gene Glyma.08G136900, which is homologous with Arabidopsis hydroxyproline-rich glycoproteins (HRGPs), may play an important role in improving the PC. Additionally, Glyma.08G136900 was divided into two main haplotype in the tested accessions. The PC of haplotype 1 was significantly lower than that of haplotype 2. The results of this study provided insights into the genetic mechanisms regulating protein content in soybean.

Research Progress in Construction and Application of Enzyme-Based DNA Logic Gates.

As a research hotspot in the field of information processing, DNA computing exhibits several important underlying characteristics-from parallel computing and low energy consumption to high-performance storage capabilities-thereby enabling its wide application in nanomachines, molecular encryption, biological detection, medical diagnosis, etc. Based on DNA computing, the most rapidly developed field focuses on DNA molecular logic-gates computing. In particular, the recent advances in enzyme-based DNA logic gates has emerged as ideal materials for constructing DNA logic gates. In this review, we explore protein enzymes that can manipulate DNA, especially, nicking enzymes and polymerases with high efficiency and specificity, which are widely used in constructing DNA logic gates, as well as ribozyme that can construct DNA logic gates following various mechanism with distinct biomaterials. Accordingly, the review highlights the characteristics and applications of various types of DNAzyme-based logic gates models, considering their future developments in information, biomedicine, chemistry, and computers.

Experimental and Simulation Study of the Fracture Instability Behavior in Polypropylene Fiber-Reinforced Concrete.

This study investigated the fracture characteristics of plain concrete and polypropylene fiber-reinforced concrete (PFRC) using pre-notched three-point bending beam tests with the digital speckle correlation method (DSCM). Then, the fracture instability behavior of the two types of beams was simulated in finite elements based on the plastic damage model and the cohesion model, for which the applicability was assessed. Furthermore, the stability of the Big Gang Mountain Dam made from plain concrete or PFRC subjected to the earth-quake loading was simulated with the plastic damage model. The results show that the limiting length of the non-local deformation zone can be used as an indicator of instability damage in a concrete structure. The simulation results of the plastic damage model agreed well with the local deformation in the pre-notched three-point bending beam test obtained from the DSCM. The plastic damage model was found to be capable of describing the residual strength phenomenon, which the cohesive model was not capable of. The damage evolution regions of the PFRC dam are strictly constrained in some regions without the occurrence of the local deformation band across the dam, and PFRC can dramatically reduce the failure risk under earthquake loading. The numerical solution proves that PFRC is an advisable material for avoiding failure in concrete dams.

Improved Bare Bones Particle Swarm Optimization for DNA Sequence Design.

DNA computing has efficient computational power, but requires high requirements on the DNA sequences used for coding, and reliable DNA sequences can effectively improve the quality of DNA encoding. And designing reliable DNA sequences is an NP problem, because it requires finding DNA sequences that satisfy multiple sets of conflicting constraints from a large solution space. To better solve the DNA sequence design problem, we propose an improved bare bones particle swarm optimization algorithm (IBPSO). The algorithm uses dynamic lensing opposition-based learning to initialize the population to improve population diversity and enhance the ability of the algorithm to jump out of local optima; An evolutionary strategy based on signal-to-noise ratio(SNR) distance is designed to balance the exploration and exploitation of the algorithm; Then an invasive weed optimization algorithm with niche crowding(NCIWO) is used to eliminate low-quality solutions and improve the search efficiency of the algorithm. In addition, we introduce the triplet-bases unpaired constraint to further improve the quality of DNA sequences. Finally, the effectiveness of the improved strategy is demonstrated by ablation experiments; and the DNA sequences designed by our algorithm are of higher quality compared with those generated by the six advanced algorithms.

DNA Sequence Optimization Design of Arithmetic Optimization Algorithm Based on Billiard Hitting Strategy.

DNA computing is a very efficient way to calculate, but it relies on high-quality DNA sequences, but it is difficult to design high-quality DNA sequences. The sequence it is looking for must meet multiple conflicting constraints at the same time to meet the requirements of DNA calculation. Therefore, we propose an improved arithmetic optimization algorithm of billiard algorithm to optimize the DNA sequence. This paper contributes as follows. The introduction to the good point set initialization to obtain high-quality solutions improves the optimization efficiency. The billiard hitting strategy was used to change the position of the population to enhance the global search scope. The use of a stochastic lens opposites learning mechanism can increase the capacity of the algorithm to get rid of locally optimal. The harmonic search algorithm is introduced to clarify some unqualified secondary structures and improve the quality of the solution. 12 benchmark functions and six other algorithms are used for comparison and ablation experiments to ensure the effectiveness of the algorithms. Finally, the DNA sequences we designed are of higher quality compared to other advanced algorithms.