Global transcriptome analysis reveals resistance genes in the early response of common bean (Phaseolus vulgaris L.) to Colletotrichum lindemuthianum.

BACKGROUND: Disease can drastically impair common bean (Phaseolus vulgaris L.) production. Anthracnose, caused by the fungal pathogen Colletotrichum lindemuthianum (Sacc. and Magnus) Briosi and Cavara, is one of the diseases that are widespread and cause serious economic loss in common bean. RESULTS: Transcriptome analysis of the early response of common bean to anthracnose was performed using two resistant genotypes, Hongyundou and Honghuayundou, and one susceptible genotype, Jingdou. A total of 9,825 differentially expressed genes (DEGs) responding to pathogen infection and anthracnose resistance were identified by differential expression analysis. By using weighted gene coexpression network analysis (WGCNA), 2,051 DEGs were found to be associated with two resistance-related modules. Among them, 463 DEGs related to anthracnose resistance were considered resistance-related candidate genes. Nineteen candidate genes were coexpressed with three resistance genes, Phvul.001G243600, Phvul.001G243700 and Phvul.001G243800. To further identify resistance genes, 46 candidate genes were selected for experimental validation using salicylic acid (SA) and methyl jasmonate (MeJA). The results indicated that 38 candidate genes that responded to SA/MeJA treatment may be involved in anthracnose resistance in common bean. CONCLUSIONS: This study identified 38 resistance-related candidate genes involved in the early response of common bean, and 19 resistance-related candidate genes were coexpressed with anthracnose resistance genes. This study identified putative resistance genes for further resistance genetic investigation and provides an important reference for anthracnose resistance breeding in common bean.

Effect of clinical whole exome sequencing in aetiological investigation and reproductive risk prediction for a couple with monogenic inherited diseases.

Objective: To determine the genetic causes of monogenic inherited diseases in a couple using clinical whole exome sequencing (WES) and advise on their reproductive choices. Methods: WES was applied to a couple seeking reproductive advice, the female with short stature and the male with congenital cataracts. Results: (1) The woman exhibited a 13.8 Kb heterozygous deletion at chrX: 591590-605428 (hg19). This region corresponds to exons 2-6 of the short-stature homeobox-containing (SHOX) gene (NM000451). Associated diseases involving the SHOX gene range from severe Leri-Weill dyschondrosteosis to mild nonspecific short stature. Meanwhile, further validation using a quantitative reverse transcription polymerase chain reaction assay confirmed the heterozygous deletion of the SHOX gene in the proband, as well as other family members with similar clinical characteristics (the proband's mother, aunt, and cousin). Multiple pathogenic reports of this variant have been included in the HGMD database. Per the American College of Medical Genetics and Genomics (ACMG) classification criteria, this deletion is classified as pathogenic. (2) For the male patient, a heterozygous variant was detected in the CRYBB3 gene: NM004076: c.226G>A (p.Gly76R). Variants in the CRYBB3 gene can cause Cataract 22 (OMIM: 609741). At present, this variant locus is not included in databases such as the gnomAD, while both SIFT and PolyPhen2 deem this locus 'damaging'. Moreover, further validation by Sanger sequencing confirmed that the variant was inherited from the male patient's mother, who also had cataracts. According to ACMG standards and guidelines, the c.226G>A (p.Gly76Arg) variant in the CRYBB3 gene is classified as having 'uncertain significance'. Conclusion: WES identified pathogenic variants in both individuals, suggesting a 25% chance of a healthy child naturally. Third-generation assisted reproductive techniques are recommended to minimize the risk of affected offspring.

LILRB2 promotes immune escape in breast cancer cells via enhanced HLA-A degradation.

PURPOSE: Increased expression of leukocyte immunoglobulin-like receptor subfamily B member 2 (LILRB2) is associated with immune evasion in breast cancer (BC). The aim of this study to elucidate the role of LILRB2 in BC progression. METHODS: LILRB2 expression in tumor tissues was detected by immunohistochemical staining. Human leukocyte antigen A (HLA-A) expression in BC cells was detected by Western blotting, and HLA-A ubiquitination was detected by immunoprecipitation and histidine pulldown assay. An in-situ tumor model was established in nude BALB/c mice to verify the role of LILRB2 in immune escape. Finally, the functions and potential mechanisms of LILRB2 in BC progression were explored using in silico data. RESULTS: LILRB2 was upregulated in BC tissues and cells, and correlated positively with poor prognosis. LILRB2 promoted BC progression by downregulating HLA-A expression. Mechanistically, LILRB2 facilitates the ubiquitination and subsequent degradation of HLA-A by promoting the interaction between the ubiquitin ligase membrane-associated ring finger protein 9 (MARCH9) and HLA-A. In syngeneic graft mouse models, LILRB2-expressing BC cells evaded CD8 + T cells and inhibited the secretion of cytokines by the cytotoxic CD8 + T cells. CONCLUSION: LILRB2 downregulates HLA-A to promote immune evasion in BC cells and is a promising new target for BC treatment.

Association between serum 25-hydroxyvitamin D level and myopia in children and adolescents: a cross-sectional study.

Background: Prior reports have indicated an inconsistent relationship between vitamin D levels and myopia in children and adolescents with limited sample size. This study was undertaken to further clarify this relationship with a repeated cross-section study. Methods: The National Health and Nutrition Examination Survey (NHANES) database with samples <19 years old was utilized. Data on rates of myopia (spherical equivalent less than or equal to -1.0 D), serum 25-hydroxyvitamin D [25(OH)D] level (high performance liquid chromatography), and other key variables were extracted and analyzed. Three models were utilized to evaluate the dose response of vitamin D levels using stepwise logistic regression. Logistic regressions for sex subgroups and other covariates were also performed, and Forest plots were drawn. Results: Data were available from 6,814 children (49.5% girls; mean age: 14.9±1.85 years). The myopia and non-myopia differed in serum 25(OH)D level, gender, race, poverty income ratio (PIR), and body mass index (BMI). Serum 25(OH)D levels were negatively correlated with myopia [odds ratio (OR) =0.98, 95% confidence interval (CI): 0.77-0.99, P<0.05] regardless of sex. Although the relationship did not appear to be linear, there was a dose effect with higher serum 25(OH)D levels linked with lower rates of myopia. In addition, rates of myopia were increased in females compared with males (OR =1.12, 95% CI: 1.01-1.24, P=0.03), those with a high PIR (OR =1.08, 95% CI: 1.04-1.11, P<0.001), and those with high BMI (OR =1.19, 95% CI: 1.11-1.27, P<0.001). White ethnicity (OR =0.78, 95% CI: 0.68-0.90, P<0.001) and leisure-time exercise (OR =0.94, 95% CI: 0.92-0.97, P=0.02) were associated with lower rates of myopia. Conclusions: These findings indicate that higher serum 25(OH)D levels and increased amounts of leisure-time exercise are associated with lower rates of myopia in this group of children and adolescents. Meanwhile, female gender, high PIR level, and high BMI were associated with greater rates of myopia. The findings indicated that children and adolescents needed leisure-time exercise to lower the risk of myopia.

Genetic analysis of albinism caused by compound heterozygous mutations of the OCA2 gene in a Chinese family.

BACKGROUND: Oculocutaneous albinism (OCA) is a group of rare genetic disorders characterized by a reduced or complete lack of melanin in the skin, hair, and eyes. Patients present with colorless retina, pale pink iris, and pupil, and fear of light. The skin, eyebrows, hair, and other body hair are white or yellowish-white. These conditions are caused by mutations in specific genes necessary for the production of melanin. OCA is divided into eight clinical types (OCA1-8), each with different clinical phenotypes and potential genetic factors. This study aimed to identify the genetic causes of non-syndromic OCA in a Chinese Han family. METHODS: We performed a comprehensive clinical examination of family members, screened for mutation loci using whole exome sequencing (WES) technology, and predicted mutations using In silico tools. RESULTS: The patient's clinical manifestations were white skin, yellow hair, a few freckles on the cheeks and bridge of the nose, decreased vision, blue iris, poorly defined optic disk borders, pigmentation of the fundus being insufficient, and significant vascular exposure. The WES test results indicate that the patient has compound heterozygous mutations in the OCA2 gene (c.1258G > A (p.G420R), c.1441G > A (p.A481T), and c.2267-2 A > C), respectively, originating from her parents. Among them, c.1258G > A (p.G420R) is a de novo mutation with pathogenic. Our analysis suggests that compound heterozygous mutations in the OCA2 gene are the primary cause of the disease in this patient. CONCLUSIONS: The widespread application of next-generation sequencing technologies such as WES in clinical practice can effectively replace conventional detection methods and assist in the diagnosis of clinical diseases more quickly and accurately. The newly discovered c.1258G > A (p.G420R) mutation can update and expand the gene mutation spectrum of OCA2-type albinism.

Application of Copy Number Variation Sequencing Technology in 422 Foetuses with Abnormal Ultrasound Soft Markers.

Purpose: The application value of ultrasound soft indicators in prenatal diagnosis was evaluated by copy number variation sequencing (CNV-seq). Methods: The authors conducted a retrospective analysis of 422 pregnant women who underwent CNV-seq testing at Luoyang Maternal and Child Health Hospital between January 2020 and November 2021. The women had presented with abnormal ultrasound soft markers; those identified as high-risk through non-invasive prenatal screening were excluded. Results: A total of 43 abnormal cases were detected in 422 pregnant women, including 24 aneuploidy (including chimerism) and 19 pathogenic or likely pathogenic copy number variations (CNVs). Based on the characteristics of ultrasound soft indicators, pregnant women were divided into five groups: isolated nuchal translucency (NT) group, combined NT group, isolated soft indicators group, combined soft indicators group and combined non-NT group. The abnormality detection rates in the five groups were 12.38% (13/105), 36.11% (13/36), 3.74% (4/103), 3.08% (2/63) and 10.09% (11/109), respectively. Statistical tests showed that the detection rate in the NT thickening combined with other abnormalities group was significantly higher than the other four groups, while there was no statistical difference in the detection rate among the other four groups. Conclusion: When NT thickening is combined with other abnormalities, it is more likely to indicate chromosome abnormalities or CNVs, so it should be regarded seriously upon finding, and pregnant women should be referred for prenatal diagnosis according to the examination results. In addition, NT thickening is an important indicator for prenatal diagnosis and should be considered regardless of whether it occurs independently. The authors recommend CNV-seq for prenatal diagnosis to prevent missing small fragments of CNVs during traditional karyotyping.

Chromosome-level genome assembly of Salvia miltiorrhiza with orange roots uncovers the role of Sm2OGD3 in catalyzing 15,16-dehydrogenation of tanshinones.

Salvia miltiorrhiza is well known for its clinical practice in treating heart and cardiovascular diseases. Its roots, used for traditional Chinese medicine materials, are usually brick-red due to accumulation of red pigments, such as tanshinone IIA and tanshinone I. Here we report a S. miltiorrhiza line (shh) with orange roots. Compared with the red roots of normal S. miltiorrhiza plants, the contents of tanshinones with a single bond at C-15,16 were increased, whereas those with a double bond at C-15,16 were significantly decreased in shh. We assembled a high-quality chromosome-level genome of shh. Phylogenomic analysis showed that the relationship between two S. miltiorrhiza lines with red roots was closer than the relationship with shh. It indicates that shh could not be the mutant of an extant S. miltiorrhiza line with red roots. Comparative genomic and transcriptomic analyses showed that a 1.0 kb DNA fragment was deleted in shh Sm2OGD3m. Complementation assay showed that overexpression of intact Sm2OGD3 in shh hairy roots recovered furan D-ring tanshinone accumulation. Consistently, in vitro protein assay showed that Sm2OGD3 catalyzed the conversion of cyptotanshinone, 15,16-dihydrotanshinone I and 1,2,15,16-tetrahydrotanshinone I into tanshinone IIA, tanshinone I and 1,2-dihydrotanshinone I, respectively. Thus, Sm2OGD3 functions as tanshinone 15,16-dehydrogenase and is a key enzyme in tanshinone biosynthesis. The results provide novel insights into the metabolic network of medicinally important tanshinone compounds.

Genome-wise association study identified genomic regions associated with drought tolerance in mungbean (Vigna radiata (L.) R. Wilczek).

KEY MESSAGE: A total of 282 mungbean accessions were resequenced to identify genome-wide variants and construct a highly precise variant map, and drought tolerance-related loci and superior alleles were identified by GWAS. Mungbean (Vigna radiata (L.) R. Wilczek) is an important food legume crop that is highly adapted to drought environments, but severe drought significantly curtails mungbean production. Here, we resequenced 282 mungbean accessions to identify genome-wide variants and constructed a highly precise map of mungbean variants. A genome-wide association study was performed to identify genomic regions for 14 drought tolerance-related traits in plants grown under stress and well-watered conditions over three years. One hundred forty-six SNPs associated with drought tolerance were detected, and 26 candidate loci associated with more than two traits were subsequently selected. Two hundred fifteen candidate genes were identified at these loci, including eleven transcription factor genes, seven protein kinase genes and other protein coding genes that may respond to drought stress. Furthermore, we identified superior alleles that were associated with drought tolerance and positively selected during the breeding process. These results provide valuable genomic resources for molecular breeding and will accelerate future efforts aimed at mungbean improvement.

TGF-ß-Induced FLRT3 Attenuation Is Essential for Cancer-Associated Fibroblast-Mediated Epithelial-Mesenchymal Transition in Colorectal Cancer.

Cancer-associated fibroblasts (CAF) constitute a major component of the tumor microenvironment. The effects of CAFs on the progression of colorectal cancer remain controversial. In this study, we found the ectopic overexpression of Fibronectin leucine-rich transmembrane protein 3 (FLRT3) inhibited the process of epithelial-mesenchymal transition (EMT), as well as the proliferation, migration, invasion, and promote apoptosis of colorectal cancer cells, whereas silencing FLRT3 expression resulted in the opposite phenomenon. FLRT3 downregulation was associated with a poor prognosis in colorectal cancer. Also, FLRT3 expression was significantly related to some clinicopathologic factors, including T stage (P = 0.037), N stage (P = 0.042), and E-cadherin (P = 0.002) level. Via univariate and multivariate analyses, M stage (P < 0.0001), FLRT3 (P = 0.044), and E-cadherin (P = 0.003) were associated with overall survival and were independent prognostic factors for it. Mechanistically, CAFs secreted TGF-ß, which downregulated FLRT3 expression by activating SMAD4 to promote aggressive phenotypes in colorectal cancer cells. Moreover, FLRT3 repressed tumorigenesis and lung metastasis, which could be reversed by LY2109761, a dual inhibitor of TGF-ß receptor type I and II. Treatment with LY2109761 increased IFN-γ expression in CD8+ T cells and reduced the number of regulatory T cells in the tumor microenvironment. Taken together, we revealed the metastasis-suppressive function of FLRT3, which was attenuated during the CAFs-mediated activation of the TGF-ß/SMAD4 signaling pathway to promote EMT in colorectal cancer. LY2109761 that significantly inhibited metastasis could be a new treatment option for advanced colorectal cancer. IMPLICATIONS: CAFs enhance colorectal cancer aggressiveness by reducing FLRT3 expression through activating TGF-ß/SMAD4 signaling pathway. CAF-targeted therapy and/or LY2109761 were promising treatments for colorectal cancer.

QTL mapping and identification of genes associated with the resistance to Acanthoscelides obtectus in cultivated common bean using a high-density genetic linkage map.

BACKGROUND: Common bean (Phaseolus vulgaris L.) is an important agricultural product with large nutritional value, and the insect pest Acanthoscelides obtectus (Say) seriously affects its product quality and commodity quality during storage. Few researches on genes of bruchid resistance have investigated in common bean cultivars. RESULTS: In this study, a bruchid-resistant cultivar black kidney bean and a highly susceptible accession Longyundou3 from different gene banks were crossed to construct a recombinant inbred line population. The genetic analysis indicated a quantitative inheritance of the bruchid resistance trait controlled by polygenes. A high-density genetic map of a total map distance of 1283.68 cM with an average interval of 0.61 cM between each marker was constructed using an F6 population of 157 recombinant inbred lines. The map has 3106 bin markers, containing 2,234,769 SNPs. Using the high-density genetic map, a new quantitative trait locus for the resistance to Acanthoscelides obtectus was identified on chromosome 6. New molecular markers based on the candidate region were developed, and this locus was further delimited to an interval of 122.3 kb between SSR markers I6-4 and I6-16 using an F2 population. This region comprised five genes. Phvul.006G003700, which encodes a bifunctional inhibitor, may be a potential candidate gene for bruchid resistance. Sequencing analysis of candidate gene identified a 5 bp insertion-deletion in promoter of gene Phvul.006G003700 between two parents. Expression analysis of candidate gene revealed that the expression level of Phvul.006G003700 in bruchid-resistant parent was markedly higher than that in bruchid-susceptible parent both in dry seeds and leaves. CONCLUSIONS: A high-density genetic linkage map was constructed utilizing whole-genome resequencing and one new QTL for bruchid resistance was identified on chromosome 6 in common bean cultivar. Phvul.006G003700 (encoding a bifunctional inhibitor) may be a potential candidate gene. These results may form the basis for further research to reveal the bruchid resistance molecular mechanism of common bean.

The aquaporin gene PvXIP1;2 conferring drought resistance identified by GWAS at seedling stage in common bean.

KEY MESSAGE: A whole-genome resequencing-derived SNP dataset used for genome-wide association analysis revealed 12 loci significantly associated with drought stress based on survival rate after drought stress at seedling stage. We further confirmed the drought-related function of an aquaporin gene (PvXIP1;2) located at Locus_10. A variety of adverse conditions, including drought stress, severely affect common bean production. Molecular breeding for drought resistance has been proposed as an effective and practical way to improve the drought resistance of common bean. A genome-wide association analysis was conducted to identify drought-related loci based on survival rates at the seedling stage using a natural population consisting of 400 common bean accessions and 3,832,340 SNPs. The coefficient of variation ranged from 40.90 to 56.22% for survival rates in three independent experiments. A total of 12 associated loci containing 89 significant SNPs were identified for survival rates at the seedling stage. Four loci overlapped in the region of the QTLs reported to be associated with drought resistance. According to the expression profiles, gene annotations and references of the functions of homologous genes in Arabidopsis, 39 genes were considered potential candidate genes selected from 199 genes annotated within all associated loci. A stable locus (Locus_10) was identified on chromosome 11, which contained LEA, aquaporin, and proline-rich protein genes. We further confirmed the drought-related function of an aquaporin (PvXIP1;2) located at Locus_10 by expression pattern analysis, phenotypic analysis of PvXIP1;2-overexpressing Arabidopsis and Agrobacterium rhizogenes-mediated hairy root transformation systems, indicating that the association results can facilitate the efficient identification of genes related to drought resistance. These loci and their candidate genes provide a foundation for crop improvement via breeding for drought resistance in common bean.

Serum ω-6/ω-3 polyunsaturated fatty acids ratio and diabetic retinopathy: A propensity score matching based case-control study in China.

BACKGROUND: Optimal ω-6/ω-3 polyunsaturated fatty acids ratio (PUFAR) is reported to exert protective effects against chronic diseases. However, data on PUFAR and diabetic retinopathy (DR) remains scarce. We aimed to thoroughly quantify whether and how PUFAR was related to DR as well as its role in DR detection. METHODS: This two-centre case-control study was conducted from August 2017 to June 2018 in China, participants were matched using a propensity score matching algorithm. We adopted multivariable logistic regression models and restricted cubic spline analyses to estimate the independent association of PUFAR with DR, adjusting for confounders identified using a directed acyclic graph. The value of PUFAR as a biomarker for DR identification was further evaluated by receiver operating characteristic analyses and Hosmer-Lemeshow tests. FINDINGS: An apparent negative relationship between PUFAR and DR was observed. Adjusted odds of DR decreased by 79% (OR: 0·21, 95% CI: 0·10-0·40) with an interquartile range increase in PUFAR. Similar results were also obtained in tertile analysis. As compared to those in the 1st tertile of PUFAR, the adjusted odds of DR decreased by 76% (OR: 0·24, 95% CI: 0·08-0·66) and 93% (OR: 0·07, 95% CI: 0·03-0·22) for subjects in the 2nd and 3rd tertiles, respectively. Good calibration and discrimination of the PUFAR associated predictive model were detected and PUFAR = 35 would be an ideal cut-off value for DR identification. INTERPRETATION: Our results suggest that serum PUAFR is inversely associated with DR. Although PUFAR-alteration is not observed amongst different stages of DR, it can serve as an ideal biomarker in distinguishing patients with DR from those without DR. FUNDING: This study was funded by Natural Science Foundation of Zhejiang Province, Zhejiang Basic Public Welfare Research Project, the Major Project of the Eye Hospital of Wenzhou Medical University, and the Academician's Science and Technology Innovation Program in Zhejiang province. Part of this work was also funded by the National Nature Science Foundation of China, and Research Project for College Students in Wenzhou Medical University.

Transcriptome Analysis of Resistance to Fusarium Wilt in Mung Bean (Vigna radiata L.).

Fusarium wilt is a destructive soil-borne disease that threatens the production of mung bean. Mung bean lines Zheng8-4 and Zheng8-20 show high resistance and high susceptibility to Fusarium wilt, respectively. Transcriptome analysis was carried out to identify candidate genes involved in Fusarium wilt resistance using Zheng8-4 and Zheng8-20 at 0, 0.5, 1, 2, and 4 days post inoculation (dpi). Differential expression analysis showed that 3,254 genes responded to pathogen infection and were differentially expressed in the resistant and susceptible lines. Weighted gene co-expression network analysis (WGCNA) was also performed to identify five modules highly correlated with Fusarium wilt resistance, in which 453 differentially expressed genes (DEGs) were considered likely to be involved in Fusarium wilt resistance. Among these DEGs, we found 24 genes encoding resistance (R) proteins, 22 encoding protein kinases, 20 belonging to transcription factor families, 34 encoding proteins with oxidoreductase activity, 17 involved in stimulation/stress responses, and 54 annotated to pathogen resistance-related pathways. Finally, 27 annotated genes were further selected as candidate genes of Fusarium wilt resistance in mung bean. This study identifies novel potential resistance-related genes against Fusarium wilt and provides a theoretical basis for further investigation of Fusarium wilt resistance in mung bean breeding.

Genetic dissection of drought resistance based on root traits at the bud stage in common bean.

KEY MESSAGE: A whole-genome resequencing-derived SNP dataset used for genome-wide association analysis revealed 196 loci significantly associated with drought stress based on root traits. Candidate genes identified in the regions of these loci include homologs of known drought resistance genes in A. thaliana. Drought is the main abiotic constraint of the production of common bean. Improved adaptation to drought environments has become a main goal of crop breeding due to the increasing scarcity of water that will occur in the future. The overall objective of our study was to identify genomic regions associated with drought resistance based on root traits using genome-wide association analysis. A natural population of 438 common bean accessions was evaluated for root traits: root surface area, root average diameter, root volume, total root length, taproot length, lateral root number, root dry weight, lateral root length, special root weight/length, using seed germination pouches under drought conditions and in well-watered environments. The coefficient of variation ranged from 11.24% (root average diameter) to 38.19% (root dry weight) in the well-watered environment and from 9.61% (root average diameter) to 39.05% (lateral root length) under drought stress. A whole-genome resequencing-derived SNP dataset revealed 196 loci containing 230 candidate SNPs associated with drought resistance. Seventeen candidate SNPs were simultaneously associated with more than two traits. Forty-one loci were simultaneously associated with more than two traits, and eleven loci were colocated with loci previously reported to be related to drought resistance. Candidate genes of the associated loci included the ABA-responsive element-binding protein family, MYB, NAC, the protein kinase superfamily, etc. These results revealed promising alleles linked to drought resistance or root traits, providing insights into the genetic basis of drought resistance and roots, which will be useful for common bean improvement.

Regulatory Mechanisms of the Resistance to Common Bacterial Blight Revealed by Transcriptomic Analysis in Common Bean (Phaseolus vulgaris L.).

Common bean blight (CBB), primarily caused by Xanthomonas axonopodis pv. phaseoli (Xap), is one of the most destructive diseases of common bean (Phaseolus vulgaris L.). The tepary bean genotype PI 319443 displays high resistance to Xap, and the common bean genotypes HR45 and Bilu display high resistance and susceptibility to Xap, respectively. To identify candidate genes related to Xap resistance, transcriptomic analysis was performed to compare gene expression levels with Xap inoculation at 0, 24, and 48 h post inoculation (hpi) among the three genotypes. A total of 1,146,009,876 high-quality clean reads were obtained. Differentially expressed gene (DEG) analysis showed that 1,688 DEGs responded to pathogen infection in the three genotypes. Weighted gene coexpression network analysis (WGCNA) was also performed to identify three modules highly correlated with Xap resistance, in which 334 DEGs were likely involved in Xap resistance. By combining differential expression analysis and WGCNA, 139 DEGs were identified as core resistance-responsive genes, including 18 genes encoding resistance (R) proteins, 19 genes belonging to transcription factor families, 63 genes encoding proteins with oxidoreductase activity, and 33 plant hormone signal transduction-related genes, which play important roles in the resistance to pathogen infection. The expression patterns of 20 DEGs were determined by quantitative real-time PCR (qRT-PCR) and confirmed the reliability of the RNA-seq results.

Selective N-glycan editing on living cell surfaces to probe glycoconjugate function.

Cell surfaces are glycosylated in various ways with high heterogeneity, which usually leads to ambiguous conclusions about glycan-involved biological functions. Here, we describe a two-step chemoenzymatic approach for N-glycan-subtype-selective editing on the surface of living cells that consists of a first 'delete' step to remove heterogeneous N-glycoforms of a certain subclass and a second 'insert' step to assemble a well-defined N-glycan back onto the pretreated glyco-sites. Such glyco-edited cells, carrying more homogeneous oligosaccharide structures, could enable precise understanding of carbohydrate-mediated functions. In particular, N-glycan-subtype-selective remodeling and imaging with different monosaccharide motifs at the non-reducing end were successfully achieved. Using a combination of the expression system of the Lec4 CHO cell line and this two-step glycan-editing approach, opioid receptor delta 1 (OPRD1) was investigated to correlate its glycostructures with the biological functions of receptor dimerization, agonist-induced signaling and internalization.

Transcriptomic analysis reveals potential genes involved in tanshinone biosynthesis in Salvia miltiorrhiza.

Tanshinones are important bioactive components in Salvia miltiorrhiza and mainly accumulate in the periderms of mature roots. Tanshinone biosynthesis is a complicated process, and little is known about the third stage of the pathway. To investigate potential genes that are responsible for tanshinone biosynthesis, we conducted transcriptome profiling analysis of two S. miltiorrhiza cultivars. Differential expression analysis provided 2,149 differentially expressed genes (DEGs) for further analysis. GO and KEGG analysis showed that the DEGs were mainly associated with the biosynthesis of secondary metabolites. Weighted gene coexpression network analysis (WGCNA) was further performed to identify a "cyan" module associated with tanshinone biosynthesis. In this module, 25 cytochromes P450 (CYPs), three 2-oxoglutarate-dependent dioxygenases (2OGDs), one short-chain alcohol dehydrogenases (SDRs) and eight transcription factors were found to be likely involved in tanshinone biosynthesis. Among these CYPs, 14 CYPs have been reported previously, and 11 CYPs were identified in this study. Expression analysis showed that four newly identified CYPs were upregulated upon application of MeJA, suggesting their possible roles in tanshinone biosynthesis. Overall, this study not only identified candidate genes involved in tanshinone biosynthesis but also provided a basis for characterization of genes involved in important active ingredients of other traditional Chinese medicinal plants.

A pro-environmental behavior model for investigating the roles of social norm, risk perception, and place attachment on adaptation strategies of climate change.

Today's climate change is a major problem and challenge for the global environment and human civilization, and it can lead to dramatical floods over specific regions. As climate change intensifies, climate change adaptation strategies, such as flood insurance, energy taxes, and other risky financial strategies, have drawn worldwide attention and discussion. Risk control methods have been widely used to mitigate the impact of climate change on past flood losses, but past risk control strategies on climate change have not focused on the exploration of the relationship between environment, society, and humans. Based on the theoretical model of pro-environmental behavior, this study compares and analyzes four theoretical models and proposes a modified competitiveness model to effectively predict the pro-environmental behavior of college students with partial least squares (PLS) manner. Social norm could play a dominant role of mediator between risk perception, place attachment, and pro-environmental behavior. Although risk perception and local attachment are positively related to risk financial strategy, the promotion of social norms will increase the intention of risk financial strategy. For intention of risk financial strategies within pro-environmental behavior, the efficiency of enhancing local attachment was higher than that of risk perception.

Application of Escherichia coli antibiotic resistance patterns for contamination source identification in watershed.

Spatial correlation of pollution of the water resource in Taipei, Taiwan, were examined by analyzing the antibiotic resistance patterns (ARPs) of 96 Escherichia coli colonies, which were isolated from 7 sampling sites in 3 river sections. The ARPs were the growth patterns of isolated E. coli colonies in the medium with seven kinds of antibiotics, including ampicillin, chlortetracycline, erythromycin, oxytetracycline, streptomycin, tetracycline, and salinomycin of different concentrations. The results showed that the survival rate of E. coli decreased with increasing concentration of antibiotics; however, various ARPs under different antibiotics of different concentrations significantly increased both the useful information and complexities. Hierarchical cluster analysis (HCA) and two-stage principal component analysis (PCA) were applied to analyze the spatial correlations and interrelations of distinct ARPs among sampling sites in this study. It was found that the seven sampling sites can be categorized into three groups which may represent three possible pollution characteristics.

Enrichment of Phosphorylated Peptides with Metal-Organic Framework Nanosheets for Serum Profiling of Diabetes and Phosphoproteomics Analysis.

Capturing phosphopeptides from complicated biological samples is essential for the discovery of new post-translational modification sites and disease diagnostics. Although several two-dimensional (2-D) materials have been used for phosphopeptides capturing, metal-organic framework (MOF) nanosheets have not been reported. The Ti-based MOF nanosheets have well-defined 2-D morphology, high density of active sites, large surface area, and an ultrathin structure. Phosphopeptides can be efficiently extracted and superior detection limits of 0.1 fmol µL-1 can be achieved even for an extremely low molar ratio of phosphoprotein/nonphosphoprotein (1:10000) mixtures. The selectivity over nonphosphopeptides can be enhanced further by pretreatment with a 10 mM salt solution (ß-glycerophosphate disodium, NaCl, or KCl). The performance of 2-D Ti-based MOF nanosheets is much better than Zr-based MOF (Zr-BTB) nanosheets or any other Ti-based 3-D MOF counterpart, such as MIL-125 and NH2-MIL-125. The nanosheets were used for in situ isotope labeling for abnormally regulated phosphopeptides analysis from serum samples of type 2 diabetes patients. The relative quantitative results showed that three of the phosphorylated fibrinogen peptides A (FPA, DpSGEGDFLAEGGGV, DpSGEGDFLAEGGGVR, and ADpSGEGDFLAEGGGVR) were down-regulated, while the other isoform (ADpSGEGDFLAEGGGV) was up-regulated in the serum samples of type 2 diabetes patients compared with those of healthy volunteers. Finally, proteomics analysis showed selective enrichment of phosphopeptides with 2-D Ti-based MOF nanosheets from real samples, including tryptic digests of mouse brain neocortex lysate, mouse spinal cord lysate, and mouse testis lysate, followed by LC-MS/MS analysis. Total numbers of 2601, 3208, and 2866 phosphopeptides were successfully identified from the three samples, respectively. The 2-D Ti-based MOF nanosheets significantly improved sample preparation for mass spectrometric analysis in phosphopeptides and phosphoproteomics research.