Genome-wide association study on resistance of cultivated soybean to Fusarium oxysporum root rot in Northeast China

BACKGROUND

Fusarium oxysporum is a prevalent fungal pathogen that diminishes soybean yield through seedling disease and root rot. Preventing Fusarium oxysporum root rot (FORR) damage entails on the identification of resistance genes and developing resistant cultivars. Therefore, conducting fine mapping and marker development for FORR resistance genes is of great significance for fostering the cultivation of resistant varieties. In this study, 350 soybean germplasm accessions, mainly from Northeast China, underwent genotyping using the SoySNP50K Illumina BeadChip, which includes 52,041 single nucleotide polymorphisms (SNPs). Their resistance to FORR was assessed in a greenhouse. Genome-wide association studies utilizing the general linear model, mixed linear model, compressed mixed linear model, and settlement of MLM under progressively exclusive relationship models were conducted to identify marker-trait associations while effectively controlling for population structure.

RESULTS

The results demonstrated that these models effectively managed population structure. Eight SNP loci significantly associated with FORR resistance in soybean were detected, primarily located on Chromosome 6. Notably, there was a strong linkage disequilibrium between the large-effect SNPs ss715595462 and ss715595463, contributing substantially to phenotypic variation. Within the genetic interval encompassing these loci, 28 genes were present, with one gene Glyma.06G088400 encoding a protein kinase family protein containing a leucine-rich repeat domain identified as a potential candidate gene in the reference genome of Williams82. Additionally, quantitative real-time reverse transcription polymerase chain reaction analysis evaluated the gene expression levels between highly resistant and susceptible accessions, focusing on primary root tissues collected at different time points after F. oxysporum inoculation. Among the examined genes, only this gene emerged as the strongest candidate associated with FORR resistance.

CONCLUSIONS

The identification of this candidate gene Glyma.06G088400 improves our understanding of soybean resistance to FORR and the markers strongly linked to resistance can be beneficial for molecular marker-assisted selection in breeding resistant soybean accessions against F. oxysporum.

Genome-wide association study of powdery mildew resistance in cultivated soybean from Northeast China

Powdery mildew (PMD), caused by the pathogen Microsphaera diffusa, leads to substantial yield decreases in susceptible soybean under favorable environmental conditions. Effective prevention of soybean PMD damage can be achieved by identifying resistance genes and developing resistant cultivars. In this study, we genotyped 331 soybean germplasm accessions, primarily from Northeast China, using the SoySNP50K BeadChip, and evaluated their resistance to PMD in a greenhouse setting. To identify marker-trait associations while effectively controlling for population structure, we conducted genome-wide association studies utilizing factored spectrally transformed linear mixed models, mixed linear models, efficient mixed-model association eXpedited, and compressed mixed linear models. The results revealed seven single nucleotide polymorphism (SNP) loci strongly associated with PMD resistance in soybean. Among these, one SNP was localized on chromosome (Chr) 14, and six SNPs with low linkage disequilibrium were localized near or in the region of previously mapped genes on Chr 16. In the reference genome of Williams82, we discovered 96 genes within the candidate region, including 17 resistance (R)-like genes, which were identified as potential candidate genes for PMD resistance. In addition, we performed quantitative real-time reverse transcription polymerase chain reaction analysis to evaluate the gene expression levels in highly resistant and susceptible genotypes, focusing on leaf tissues collected at different times after M. diffusa inoculation. Among the examined genes, three R-like genes, including Glyma.16G210800, Glyma.16G212300, and Glyma.16G213900, were identified as strong candidates associated with PMD resistance. This discovery can significantly enhance our understanding of soybean resistance to PMD. Furthermore, the significant SNPs strongly associated with resistance can serve as valuable markers for genetic improvement in breeding M. diffusa-resistant soybean cultivars.

Neural Network With a Preference Sampling Paradigm for Imbalanced Data Classification

Most data in real life are characterized by imbalance problems. One of the classic models for dealing with imbalanced data is neural networks. However, the data imbalance problem often causes the neural network to display negative class preference behavior. Using an undersampling strategy to reconstruct a balanced dataset is one of the methods to alleviate the data imbalance problem. However, most existing undersampling methods focus more on the data or aim to preserve the overall structural characteristics of the negative class through potential energy estimation, while the problems of gradient inundation and insufficient empirical representation of positive samples have not been well considered. Therefore, a new paradigm for solving the data imbalance problem is proposed. Specifically, to solve the problem of gradient inundation, an informative undersampling strategy is derived from the performance degradation and used to restore the ability of neural networks to work under imbalanced data. In addition, to alleviate the problem of insufficient empirical representation of positive samples, a boundary expansion strategy with linear interpolation and the prediction consistency constraint is considered. We tested the proposed paradigm on 34 imbalanced datasets with imbalance ratios ranging from 16.90 to 100.14. The test results show that our paradigm obtained the best area under the receiver operating characteristic curve (AUC) on 26 datasets.

Identification of novel monoclonal antibodies targeting the outer membrane protein C and lipopolysaccharides for Escherichia coli O157:H7 detection

AIMS

To identify and evaluate the application of two novel monoclonal antibody (mAb) 2G12 against outer membrane protein (Omp) C and mAb 12B1 targeting the O chain of the lipopolysaccharides (LPS) of Escherichia coli O157:H7 (ECO157).

METHODS AND RESULTS

The sensitivity and specificity of these two antibodies were evaluated with eight ECO157 strains and 68 untargeted strains. mAb 2G12 and 12B1 had no detectable binding with any of the non-O157 strains at 6·0 log₁₀ CFU per ml, while its high specificity and affinity remained with all ECO157 strains. When a higher level (8·0 log₁₀ CFU per ml) was tested, 2G12 and 12B1 did not react with 82·35 and 97·06% of the non-O157 strains respectively. Based on the pair of two antibodies, the sandwich enzyme-linked immunosorbent assay detected 100% (8/8) of ECO157 strains and none of the non-ECO157 strains. The detection limit of ECO157 strains in pure culture were 4·2 ± 0·2 log₁₀ CFU per ml. When the developed test was applied to artificially inoculated beef samples, the detection limit was 6·0 log₁₀ CFU per gram without enrichment and 1·0 log₁₀ CFU per gram after 12 h of enrichment.

CONCLUSIONS

The two novel antibodies identified in this study served as great candidates for the recovery, and detection of ECO157 from different environmental and food samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

ECO157-specific detection was improved by a combination of the novel OmpC mAb and LPS mAb with defined target antigen and good specificity.

Multi-View Linear Discriminant Analysis Network

In many real-world applications, an object can be described from multiple views or styles, leading to the emerging multi-view analysis. To eliminate the complicated (usually highly nonlinear) view discrepancy for favorable cross-view recognition and retrieval, we propose a Multi-view Linear Discriminant Analysis Network (MvLDAN) by seeking a nonlinear discriminant and view-invariant representation shared among multiple views. Unlike existing multi-view methods which directly learn a common space to reduce the view gap, our MvLDAN employs multiple feedforward neural networks (one for each view) and a novel eigenvalue-based multi-view objective function to encapsulate as much discriminative variance as possible into all the available common feature dimensions. With the proposed objective function, the MvLDAN could produce representations possessing: 1) low variance within the same class regardless of view discrepancy, 2) high variance between different classes regardless of view discrepancy, and 3) high covariance between any two views. In brief, in the learned multi-view space, the obtained deep features can be projected into a latent common space in which the samples from the same class are as close to each other as possible (even though they are from different views), and the samples from different classes are as far from each other as possible (even though they are from the same view). The effectiveness of the proposed method is verified by extensive experiments carried out on five databases, in comparison with the 19 state-of-the-art approaches.

Combined cytotoxicity of aflatoxin B1 and deoxynivalenol to hepatoma HepG2/C3A cells

Co-occurrence of aflatoxin B1 (AFB1) and deoxynivalenol (DON) is one of the most common mycotoxin contaminations in cereal crops and food ingredients. However, the mechanism of their combined toxicity is poorly understood. In the current investigation, the hepatoma HepG2/C3A cell line was used to explore the combined cytotoxicity of AFB1 and DON. The values of IC50, based on a sulforhodamine B (SRB) assay, were 4.5 mM and 18.7 mM for DON and AFB1, respectively. The analysis of cytotoxicity endpoints using the combination index (CI) theory revealed that the changes of mitochondrial membrane permeability and ATP resulted from an additive cytotoxic effect (CI≈1) of AFB1 and DON. However, the endpoints of double strand DNA (ds-DNA), reactive oxygen species (ROS) and cell viability (SRB) were synergistically (CI<1) affected in a dose-dependent manner. RNA-seq analysis demonstrated a number of uniquely expressed genes in their combination (AFB1: 2.5 mM, DON: 0.56 mM), indicating a synergistic interaction between AFB1 and DON at a molecular level. Additional transcriptomics analysis showed that the endoplasmic reticulum stress-associated JNK/p38/MAPK pathway was induced by DON, whereas the p53 signalling pathway was activated by AFB1. The expression profiles of apoptosis-related genes caspase-3, Bax and Bcl-2 suggested a mitochondria-mediated apoptosis pathway that was shared between AFB1 and DON. Thus, different cytotoxicity pathways and their converging at the apoptotic process might be the mechanism of the additive/synergistic cytotoxicity of AFB1 and DON to HepG2/C3A cells.

Disorder dependence of the ferromagnetic quantum phase transition

We quantitatively discuss the influence of quenched disorder on the ferromagnetic quantum phase transition in metals, using a theory that describes the coupling of the magnetization to gapless fermionic excitations. In clean systems, the transition is first order below a tricritical temperature T_{tc}. Quenched disorder is predicted to suppress T_{tc} until it vanishes for residual resistivities ρ_{0} on the order of several μΩ cm for typical quantum ferromagnets. We discuss experiments that allow us to distinguish the mechanism considered from other possible realizations of a first-order transition.

Neutrophil-lymphocyte ratio: a novel predictor for short-term prognosis in acute-on-chronic hepatitis B liver failure

Acute-on-chronic hepatitis B liver failure (ACHBLF) has a poor prognosis in patients with hepatitis B virus infection. The role of the neutrophil-lymphocyte ratio (NLR), which reflects the inflammatory status of the patient before treatment, has never been studied in this setting. To investigate the predictive value of NLR in patients with ACHBLF, a retrospective cohort with 216 patients and a prospective validation cohort with 73 patients were recruited. Multivariate analyses showed that total bilirubin (TBIL), NLR, age and model for end-stage liver disease (MELD) score had prognostic significance for survival. Both NLR (0.781) and MELD score (0.744) had higher ROC curves, which differed significantly from those for age (0.615) and TBIL (0.691), but not from each other (P = 0.94). NLR ≤ 2.36 predicted lower mortality (with 91.6% sensitivity and 86.0% negative predictive value), and NLR >6.12 was a warning sign for higher mortality risk (with 90.1% specificity and 80.3% positive predictive value). These results demonstrated that pretreatment NLR was associated with the prognosis of patients with ACHBLF, and elevated NLR predicted poor outcome within 8 weeks. We suggest that NLR cut-offs of ≤ 2.36 and >6.12 are powerful markers for predicting mortality in ACHBLF.

hSSB1 binds and protects p21 from ubiquitin-mediated degradation and positively correlates with p21 in human hepatocellular carcinomas

Downregulation of hSSB1, a single-stranded DNA-binding protein, causes increased radiosensitivity, defective checkpoint activation and genomic instability. However, the mechanisms of hSSB1 function in these responses remain to be uncovered. Here, we present evidence that hSSB1 directly binds p21 and this interaction may prevent p21 from ubiquitin-mediated degradation. Furthermore, both promotion of the G1/S transition and abrogation of the G2/M checkpoints induced by hSSB1 knockdown are partially dependent on p21. Most importantly, hSSB1 and p21 levels are positively correlated in human hepatocellular carcinomas (HCC), as determined by immunostaining. Therefore, hSSB1 may positively modulate p21 to regulate cell cycle progression and DNA damage response, implicating hSSB1 as a novel, promising therapeutic target for cancers such as HCC.

Thermal effects on atomic friction

We model friction acting on the tip of an atomic force microscope as it is dragged across a surface at nonzero temperatures. We find that stick-slip motion occurs and that the average frictional force follows (absolute value lnv)(2/3), where v is the tip velocity. This compares well to recent experimental work, permitting the quantitative extraction of all microscopic parameters. We calculate the scaled form of the average frictional force's dependence on both temperature and tip speed as well as the form of the friction-force distribution function.

Regulation of plant water loss by manipulating the expression of phospholipase Dalpha

Phospholipase D (PLD) has been implicated in various processes, including signal transduction, membrane trafficking, and membrane degradation. Multiple forms of PLD with distinct biochemical properties have been described in the cell. In Arabidopsis, PLDalpha and PLDgamma, but not PLDbeta, were detected in guard cells, and antisense suppression resulted in a specific loss of PLDalpha. The abrogation of PLDalpha rendered plants less sensitive to abscisic acid and impaired stomatal closure induced by water deficits. PLDalpha-depleted plants exhibited accelerated transpirational water loss and a decreased ability to tolerate drought stress. Overexpression of PLDalpha enhanced the leaf's sensitivity to abscisic acid. These findings provide molecular and physiological evidence that PLDalpha plays a crucial role in regulating stomatal movement and plant-water status.

Phospholipase D and phosphatidic acid-mediated generation of superoxide in Arabidopsis

Phospholipase D (PLD), which hydrolyzes phospholipids into free head groups and phosphatidic acid (PA), may regulate cellular processes through the production of lipid and lipid-derived messengers. We have genetically abrogated PLD alpha, the most prevalent isoform of PLD in plants, and the depletion of PLD alpha in Arabidopsis decreased the levels of PA and superoxide production in Arabidopsis leaf extracts. Addition of PA promoted the synthesis of superoxide in the PLD alpha-depleted plants, as measured by chemiluminescence and superoxide dismutase-inhibitable, NADPH-dependent reduction of cytochrome c and nitroblue tetrazolium. The PA-enhanced generation of superoxide was associated mainly with microsomal membranes. Among various lipids tested, PA was the most effective stimulator with the optimal concentrations between 100 and 200 microM. The PA-promoted production of superoxide was observed also in leaves directly infiltrated with PA. The added PA was more effective in stimulating superoxide generation in the PLD alpha-depleted leaves than in the PLD alpha-containing, wild-type leaves, suggesting that PA produced in the cell was more effective than added PA in promoting superoxide production. These data indicate that PLD plays a role in mediating superoxide production in plants through the generation of PA as a lipid messenger.

Relationship between HLA-DRB1 and DQ alleles and the genetic susceptibility to type 1 diabetes

OBJECTIVE

To study the relationship between human leukocyte antigen (HLA)-DRB1 and DQ alleles and the genetic susceptibility of type 1 diabetes in North Chinese children.

METHODS

Polymerase chain reaction (PCR) techniques were used to amplify the second exon of DRB1 and DQ alleles, after which sequence specific olignucleotide probe (SSOP) dot blot hybridization techniques were used to analyze the amplified products.

RESULTS

DRB1 * 0301, DQA1 * 0301, DQB1 * 0201 alleles and DRB1 * 0301-DQA1 * 0501-DQB1 * 0201 haplotype were significantly increased in patients, while DQA1 * 0103 and DQB1 * 0601 alleles were significantly increased in controls. The distribution of DR4 and DR9 haplotypes in patients and controls were not significantly different, but DR3/DR4 and DR4/DR9 heterozygotes were significantly increased in patients.

CONCLUSIONS

DRB1 * 0301, DQA1 * 0301 and DQB1 * 0201 confer susceptibility while DQA1 * 0103 and DQB1 * 0601 confer protection to type 1 diabetes. DRB1 * 0301-DQA1 * 0501-DQB1 * 0201 haplotype offers a predisposition to type 1 diabetes in North Chinese. Although the distribution of DR4 and DR9 in patients and controls had no significant difference, DR3/DR4 and DR3/DR9 heterozygotes were significantly increased in patients, showing that the susceptive effects of DR3 and DR4 or DR4 and DR9 haplotypes could be added up.

Determining functions of multiple phospholipase Ds in stress response of Arabidopsis

Phospholipase D (PLD) is encoded by a multiple gene family, and several PLDs from Arabidopsis have been characterized at the molecular biological and biochemical levels. PLDalpha is the most abundant plant PLD and exhibits a number of different biochemical properties to the other isoforms. The other PLDs have many overlapping catalytic properties but display some unique patterns of expression during development and in response to stress cues. Accumulating data indicate that different PLDs have multiple and different roles in plant responses to stress.

Comparative physical mapping of the 18S-5.8S-26S rDNA in three sorghum species

The physical locations of the 18S-5.8S-26S rDNA sequences were examined in three sorghum species by fluorescence in situ hybridization (FISH) using biotin-labeled heterologous 18S-5.8S-26S rDNA probe (pTa71). Each 18S-5.8S-26S rDNA locus occurred at two sites on the chromosomes in Sorghum bicolor (2n = 20) and S. versicolor (2n = 10), but at four sites on the chromosomes of S. halepense (2n = 40) and the tetraploid S. versicolor (2n = 20). Positions of the rDNA loci varied from the interstitial to terminal position among the four accessions of the three sorghum species. The rDNA data are useful for investigation of chromosome evolution and phylogeny. This study excluded S. versicolor as the possible progenitor of S. bicolor.

[Effects of tangshenkang capsule on diabetic nephropathy]

To study the effects of Chinese herbal medicine Tangshenkang (TSK) capsule on diabetic nephropathy (DN), 57 patients with DN were randomly divided into two groups, the treated group and the control group, they were treated with TSK capsule and the conventional therapy respectively. There were serious disorders of metabolism in DN patients, that showed the TXB 2/6-keto-PGF1 alpha ratios and lipid peroxidase (LPO) levels were higher than that of healthy people. After 6 weeks treated with TSK capsule the albuminuria levels reduced obviously (decreased 51%), renal plasma flow (RPF) increased, glomerular filtration rate and the LPO levels decreased and a positive correlation was observed between albuminuria levels and TXB 2/6-keto-PGF1 alpha ratios while the clearance rate of creafinin didn't improve significantly. There were no significant difference in the above-mentioned parameters in the control group before and after treatment. These results suggested that TSK capsule possessed a significant effect in improving albuminuria and glomerular function. And the effect of TSK might be due to its adjusting TXB 2/6-keto-PGF1 alpha ratios and its lipid-peroxidation in DN patients.

A model of solar energetic particles for use in calculating LET spectra developed from ONR-604 data

A model of solar energetic particles (SEP) has been developed and is applied to solar flares during the 1990/1991 CRRES mission using data measured by the University of Chicago instrument, ONR-604. The model includes the time-dependent behavior, heavy-ion content, energy spectrum and fluence, and can accurately represent the observed SEP events in the energy range between 40 to 500 MeV/nucleon. Results are presented for the March and June, 1991 flare periods.

A model of galactic cosmic rays for use in calculating linear energy transfer spectra

The galactic cosmic rays (GCR) contain fully stripped nuclei, from Hydrogen to beyond the Iron group, accelerated to high energies and are a major component of the background radiation encountered by satellites and interplanetary spacecraft. This paper presents a GCR model which is based upon our current understanding of the astrophysics of GCR transport through interstellar and interplanetary space. The model can be used to predict the energy spectra for all stable and long-lived radioactive species from H to Ni over an energy range from 50 to 50,000 MeV/nucleon as a function of a single parameter, the solar modulation level phi. The details of this model are summarized, phi is derived for the period 1974 to present, and results from this model during the 1990/1991 CRRES mission are presented.