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1.
Front Plant Sci ; 12: 751891, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34721480

RESUMO

Conifers are the world's major source of timber and pulpwood and have great economic and ecological value. Currently, little research on the application of CRISPR/Cas9, the commonly used genome-editing tool in angiosperms, has been reported in coniferous species. An efficient CRISPR/Cas9 system based on somatic embryogenesis (SEis) suitable for conifers could benefit both fundamental and applied research in these species. In this study, the SpCas9 gene was optimized based on codon bias in white spruce, and a spruce U6 promoter was cloned and function-validated for use in a conifer specific CRISPR/Cas9 toolbox, i.e., PgCas9/PaU6. With this toolbox, a genome-editing vector was constructed to target the DXS1 gene of white spruce. By Agrobacterium-mediated transformation, the genome-editing vector was then transferred into embryogenic tissue of white spruce. Three resistant embryogenic tissues were obtained and used for regenerating plants via SEis. Albino somatic embryo (SE) plants with mutations in DXS1 were obtained in all of the three events, and the ratios of the homozygous and biallelic mutants in the 18 albino mutants detected were 22.2% in both cases. Green plants with mutations in DXS1 were also produced, and the ratios of the DXS1 mutants to the total green plants were 7.9, 28, and 13.5%, respectively, among the three events. Since 22.7% of the total 44 mutants were edited at both of the target sites 1 and 2, the CRISPR/Cas9 toolbox in this research could be used for multi-sites genome editing. More than 2,000 SE plants were regenerated in vitro after genome editing, and part of them showed differences in plant development. Both chimerism and mosaicism were found in the SE plants of white spruce after genome editing with the CRISPR/Cas9 toolbox. The conifer-specific CRISPR/Cas9 system developed in this research could be valuable in gene function research and trait improvement.

2.
PeerJ ; 9: e12276, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34721975

RESUMO

Background: Breast invasive carcinoma (BRCA) is a commonly occurring malignant tumor. Zinc finger proteins (ZNFs) constitute the largest transcription factor family in the human genome and play a mechanistic role in many cancers' development. The prognostic value of ZNFs has yet to be approached systematically for BRCA. Methods: We analyzed the data of a training set from The Cancer Genome Atlas (TCGA) database and two validation cohort from GSE20685 and METABRIC datasets, composed of 3,231 BRCA patients. After screening the differentially expressed ZNFs, univariate Cox regression, LASSO, and multiple Cox regression analysis were performed to construct a risk-based predictive model. ESTIMATE algorithm, single-sample gene set enrichment analysis (ssGSEA), and gene set enrichment analyses (GSEA) were utilized to assess the potential relations among the tumor immune microenvironment and ZNFs in BRCA. Results: In this study, we profiled ZNF expression in TCGA based BRCA cohort and developed a novel prognostic model based on 14 genes with ZNF relations. This model was composed of high and low-score groups for BRCA classification. Based upon Kaplan-Meier survival curves, risk-status-based prognosis illustrated significant differences. We integrated the 14 ZNF-gene signature with patient clinicopathological data for nomogram construction with accurate 1-, 3-, and 5-overall survival predictive capabilities. We then accessed the Genomics of Drug Sensitivity in Cancer database for therapeutic drug response prediction of signature-defined BRCA patient groupings for our selected TCGA population. The signature also predicts sensitivity to chemotherapeutic and molecular-targeted agents in high- and low-risk patients afflicted with BRCA. Functional analysis suggested JAK STAT, VEGF, MAPK, NOTCH TOLL-like receptor, NOD-like receptor signaling pathways, apoptosis, and cancer-based pathways could be key for ZNF-related BRCA development. Interestingly, based on the results of ESTIMATE, ssGSEA, and GSEA analysis, we elucidated that our ZNF-gene signature had pivotal regulatory effects on the tumor immune microenvironment for BRCA. Conclusion: Our findings shed light on the potential contribution of ZNFs to the pathogenesis of BRCA and may inform clinical practice to guide individualized treatment.

3.
Int J Gen Med ; 14: 7371-7380, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34744450

RESUMO

Purpose: Although the burden of breast cancer remains especially high in rural China, data on the clinicopathological characteristics and prevalence of the breast cancer susceptibility gene 1/2 (BRCA1/2) mutations in patients with breast cancer remain limited. We investigated the clinicopathological characteristics, changing patterns, and prevalence of BRCA1/2 mutations in patients with breast cancer. Patients and Methods: The clinicopathological characteristics of 3712 women with pathologically confirmed primary breast cancer treated at Meizhou People's Hospital between January 2005 and December 2018 were evaluated. The prevalence of BRCA1/2 mutations in 340 patients with breast cancer diagnosed between January 2017 and September 2018 was also evaluated. Results: The median age at diagnosis was 49±10.5 (range, 20-94) years. Positivity for estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) was observed in 59.0%, 52.5%, and 24.9% of patients, respectively. Time trend analysis revealed that an increasing trend was observed for age at diagnosis (p = 0.001), proportion of patients without a reproductive history (p < 0.001), postmenopausal patients (p = 0.001), invasive pathological cancer type (p = 0.008), ER-positive rate (p < 0.001), PR-positive rate (p = 0.008), and HER2-positive rate (p < 0.001). Compared with patients without BRCA1/2 mutations, those with BRCA1/2 mutations were more likely to have a family history of breast or ovarian cancer (p < 0.001) and have triple-negative breast cancer (TNBC) (p < 0.001). Family history of breast or ovarian cancer (odds ratio [OR], 103.58; 95% confidence interval [CI], 20.58-521.45; p < 0.001) and TNBC subtype (OR, 5.97; 95% CI, 1.16-30.90; p = 0.033) were independent predictors for BRCA1/2 mutation. Conclusion: The clinicopathological characteristics of patients with breast cancer in this rural area have changed during the past decade. BRCA1/2 testing should be performed in patients with breast cancer with a family history of breast or ovarian cancer and TNBC.

4.
Bioengineered ; 2021 Nov 17.
Artigo em Inglês | MEDLINE | ID: mdl-34787047

RESUMO

Long non-coding RNA (lncRNA) prostate cancer-associated transcript 18 (PCAT18) is a potential diagnostic target for adenocarcinoma. However, its role in triple-negative breast cancer (TNBC) remains largely unknown. Based on data from an online database, a significant decline in lncRNA PCAT18 was observed in patients with TNBC subtype compared to a population with normal breast tissue. Patients with TNBC with high PCAT18 levels presented good outcomes. Patients with TNBC with high PCAT18 had a lower rate of lymph node-positive metastasis than those with low PCAT18. PCAT18-upregulation inhibited, while PCAT18-downregulation promoted, migration and expression of matrix metalloproteinases 9/2 (MMP9/MMP2) and uridylyl phosphate adenosine (uPA) in TNBC cells. Activating transcription factor 7 (ATF7) was positively associated with PCAT18, and ATF7-inhibition abrogated the anti-migration effects of PCAT18 on TNBC cells. Mechanistically, miR-103a-3p directly targeted and inhibited ATF7 expression. PCAT18 competitively sponges miR-103a-3p, promoting the expression of ATF7. Exogenous PCAT18 was associated with lower incidence of lung metastasis followed by the upregulation of ATF7, which was prevented by the treatment of miR-103a-3p mimics. Collectively, PCAT18 was expressed at low levels in TNBC, and PCAT18 could sponge miR-103a-3p and promote ATF7 expression, resulting in prevention of TNBC metastasis. Thus, PCAT18 can serve as a predictive factor for patients with metastatic TNBC.Graphical abstract:[Figure: see text].

5.
J Colloid Interface Sci ; 608(Pt 2): 1846-1856, 2021 Oct 16.
Artigo em Inglês | MEDLINE | ID: mdl-34742093

RESUMO

The formation of interfacial chemical bonding in heterostructures plays an important role in the transport of carriers. Herein, we firstly prepared ultrathin InVO4 nanosheet (Ns) with a thickness of 1.5 nm. Diethylenetriamine-modified CdSe (CdSe-DETA) nanobelts are in-situ deposited on the surface of ultrathin InVO4 Ns to build a InVO4/CdSe-DETA step-scheme (S-scheme) heterojunction photocatalysts. The protonated DETA acts as an amine-bridge to promote the formation of a tight chemical bond at the interface of InVO4/CdSe-DETA, thereby promoting the transfer of carriers at the interface. For photocatalytic CO2 reduction, the rationally designed InVO4/CdSe-DETA S-scheme photocatalyst exhibits a remarkable CO generation rate of 27.9 µmol h-1 g-1 at 420 nm, which is 3.35 and 3.39 times higher than that of CdSe-DETA and InVO4 Ns, respectively. The new method by using interfacial chemical bonding to facilitate interfacial charge transportation provide a promising strategy for improve photocatalysis.

6.
J Histochem Cytochem ; : 221554211058098, 2021 Nov 09.
Artigo em Inglês | MEDLINE | ID: mdl-34751042

RESUMO

The poor clinical prognosis and microvascular patterns of glioblastoma (GBM) are of serious concern to many clinicians and researchers. However, very few studies have examined the correlation between microvascular niche patterns (MVNPs) and proteomic distribution. In this study, CD34 immunofluorescence staining and matrix-assisted laser desorption ionization-mass spectrometry imaging (MALDI-IMS) technology were used to investigate the protein distributions in MVNPs. CD34+ microvascular phenotype could be divided into four types: microvascular sprouting (MS), vascular cluster (VC), vascular garland (VG), and glomeruloid vascular proliferation (GVP). Based on such characteristics, MVNPs were divided into two types by cluster analysis, namely, type I, comprising primarily MS and VC, and type II, comprising many VGs and GVPs. Survival analysis indicated the type of MVNPs to be an independent prognostic factor for progression-free and overall survival in GBM. MALDI-IMS results showed the peaks at m/z 1037 and 8960 to exhibit stronger ion signals in type II, while those at m/z 3240 and 3265 exhibited stronger ion signals in type I. The findings may assist future research on therapy and help predict prognosis in GBM. However, due to the limited number of studies, more well-designed studies are warranted to further verify our results.

7.
J Med Chem ; 2021 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-34783558

RESUMO

Adenosine is an immunosuppressive factor in the tumor microenvironment mainly through activation of the A2A adenosine receptor (A2AR), which is a mechanism hijacked by tumors to escape immune surveillance. Small-molecule A2AR antagonists are being evaluated in clinical trials as immunotherapeutic agents, but their efficacy is limited as standalone therapies. To enhance the antitumor effects of A2AR antagonists, dual-acting compounds incorporating A2AR antagonism and histone deacetylase (HDAC) inhibitory actions were designed and synthesized, based on co-crystal structures of A2AR. Compound 24e (IHCH-3064) exhibited potent binding to A2AR (Ki = 2.2 nM) and selective inhibition of HDAC1 (IC50 = 80.2 nM), with good antiproliferative activity against tumor cell lines in vitro. Intraperitoneal administration of 24e (60 mg/kg, bid) inhibited mouse MC38 tumor growth with a tumor growth inhibition rate of 95.3%. These results showed that dual-acting compounds targeting A2AR and HDAC are potentially immunotherapeutic agents that are worth further exploring.

8.
Toxicol Lett ; 353: 1-12, 2021 Oct 06.
Artigo em Inglês | MEDLINE | ID: mdl-34626813

RESUMO

Silicosis as the serious occupational disease is highly necessary to construct a suitable mouse model for disclosing mechanism of occurrence and development in this disease. Here, the volume-effect relationship and volume-based survival curves in mice who inhaled silica suspension intranasally were analyzed. Notable, the optimal volume 80 µl repeated-inhalation by nose to silica suspension in the inbred mouse C57BL/6 J with the highest susceptibility to silicosis led to a great entrance into the lung and a high survival rate after instillation. After repeated-exposure to 20 mg/mL, 80 µl silica for 16 days and then fed without silica exposure until 31 days, weight of mice showed a trend of first decrease and then recover. Moreover, the degree of pulmonary inflammation and fibrosis in mice were analyzed by pathological and immunohistochemistry staining. Transforming growth factor-beta (TGF-ß), smooth muscle alpha-actin (α-SMA) and collagen type-I (collagen I, Col-I) were significantly increased in the silica-exposed mouse lung at post-exposure day 16 compared with the controls. Sirius red stain and Micro-CT analysis showed that lung fibrosis formed at post-exposure day 31. This study highlights the critical importance of perfusion volume and repeated nasal drops in inducing inflammatory response and pulmonary fibrosis in silicosis.

9.
Adv Mater ; : e2106354, 2021 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-34699632

RESUMO

CO2 electroreduction (CO2 RR) to CO is promising for carbon cycle but still remains challenging. Au is regarded as the most selective catalyst for CO2 RR, while the high cost significantly hinders its industrial application. Herein, the bimetallic CuInSe2 is found to exhibit an Au-like catalytic feature: i) the interaction of Cu and In orbitals induces a moderate adsorption strength of CO2 RR intermediates and favors the reaction pathway; ii) the hydrogen evolution is energetically unfavorable on CuInSe2 , as a surface reconstruction along with high energy change will occur after hydrogen adsorption. Furthermore, the Se vacancy is found to induce an electron re-distribution, slightly tune the band structure and optimize the CO2 RR route of bimetallic selenide. Consequently, the Se-defective CuInSe2 (V-CuInSe2 ) achieves a highly selective CO production ability that comparable to noble metals in aqueous electrolyte, and the V-CuInSe2 cathode shows a satisfactory performance in an aqueous Zn-CO2 cell. This work demonstrates that designing cost-effective catalysts with noble metal-like properties is an ideal strategy for developing efficient electrocatalysts. Moreover, the class of transition bimetallic selenides have shown promising prospects as active and cost-effective electrocatalysts owing to their unique the structural, electronic and catalytic properties. This article is protected by copyright. All rights reserved.

10.
Adv Sci (Weinh) ; : e2102970, 2021 Oct 27.
Artigo em Inglês | MEDLINE | ID: mdl-34705318

RESUMO

The development of simple, efficient, and biocompatible organic luminescent molecules is of great significance to the clinical transformation of biomaterials. In recent years, purely organic thermally activated delayed fluorescence (TADF) materials with an extremely small single-triplet energy gap (ΔEST ) have been considered as the most promising new-generation electroluminescence emitters, which is an enormous breakthrough in organic optoelectronics. By merits of the unique photophysical properties, high structure flexibility, and reduced health risks, such metal-free TADF luminophores have attracted tremendous attention in biomedical fields, including conventional fluorescence imaging, time-resolved imaging and sensing, and photodynamic therapy. However, there is currently no systematic summary of the TADF materials for biomedical applications, which is presented in this review. Besides a brief introduction of the major developments of TADF material, the typical TADF mechanisms and fundamental principles on design strategies of TADF molecules and nanomaterials are subsequently described. Importantly, a specific emphasis is placed on the discussion of TADF materials for various biomedical applications. Finally, the authors make a forecast of the remaining challenges and future developments. This review provides insightful perspectives and clear prospects towards the rapid development of TADF materials in biomedicine, which will be highly valuable to exploit new luminescent materials.

11.
Adv Mater ; : e2106973, 2021 Oct 22.
Artigo em Inglês | MEDLINE | ID: mdl-34676920

RESUMO

Crystal structure engineering of nanomaterials is crucial for the design of electrocatalysts. Inducing dislocations is an efficient approach to generate strain effects in nanomaterials to optimize the crystal and electronic structures and improve the catalytic properties. However, it is almost impossible to produce and retain dislocations in commercial mainstream catalysts, such as single metal platinum (Pt) catalysts. In this work, a non-equilibrium high-temperature (>1400 K) thermal-shock method is reported to induce rich dislocations in Pt nanocrystals (Dr-Pt). The method is performed in an extreme environment (≈77 K) created by liquid nitrogen. The dislocations induced within milliseconds by thermal and structural stress during the crystallization process are kinetically frozen at an ultrafast cooling rate. The high-energy surface structures with dislocation-induced strain effects can prevent surface restructuring during catalysis. The findings indicate that a novel extreme environmental high-temperature thermal-shock method can successfully introduce rich dislocations in Pt nanoparticles and significantly boost its hydrogen evolution reaction performance.

12.
PLoS One ; 16(10): e0257072, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34597305

RESUMO

Liver cancer morbidity and mortality rates differ among ethnic groups. In the United States, the burden of liver cancer in Asian Americans (AS) is higher compared to Caucasian Americans (CA). Research on liver cancer health disparities has mainly focused on environmental and socioeconomic factors yet has ignored the genotypic differences among various racial/ethnic groups. This lack of molecular level understanding has hindered the development of personalized medical approaches for liver cancer treatment. To understand the genetic heterogeneity of liver cancer between AS and CA, we performed a systematic analysis of RNA-seq data of AS and CA patients from The Cancer Genome Atlas (TCGA). We used four differential gene expression analysis packages; DESeq2, limma, edgeR, and Superdelta2, to identify the differentially expressed genes. Our analysis identified cytochrome P450-2D6 enzyme (CYP2D6) as the gene with the greatest differential expression with higher levels in AS compared to CA. To scrutinize the underlying mechanism of CYP2D6, Ingenuity Pathway Analysis (IPA) and Cytoscape were conducted and found hepatocyte nuclear factor-4α (HNF4A) and interleukin-6 (IL6) in direct association with CYP2D6. IL6 is downregulated in AS compared to CA, while HNF4A is not significantly different. Herein, we report that CYP2D6 may serve as a putative biomarker in liver cancer health disparities. Its negative association with IL6 proclaims an intricate relationship between CYP2D6 and inflammation in the ethnic differences seen in AS and CA liver cancer patients. The goal of the present study was to understand how genetic factors may contribute to the interethnic variability of liver cancer prevalence and outcomes in AS and CA patients. Identifying ethnic-specific genes may help ameliorate detection, diagnosis, surveillance, and treatments of liver cancer, as well as reduce disease-related incidence and mortality rates in the vulnerable population.


Assuntos
Carcinoma Hepatocelular/genética , Citocromo P-450 CYP2D6/genética , Regulação Neoplásica da Expressão Gênica , Genótipo , Neoplasias Hepáticas/genética , Polimorfismo Genético , Alelos , Biomarcadores Tumorais/genética , Carcinoma Hepatocelular/mortalidade , Carcinoma Hepatocelular/patologia , Bases de Dados Genéticas , Perfilação da Expressão Gênica , Redes Reguladoras de Genes , Disparidades nos Níveis de Saúde , Humanos , Neoplasias Hepáticas/mortalidade , Neoplasias Hepáticas/patologia
13.
Org Lett ; 23(22): 8662-8667, 2021 Nov 19.
Artigo em Inglês | MEDLINE | ID: mdl-34714098

RESUMO

We report the synthesis of polysubstituted 1,1,2,3-tetraarylazulen-6-ones through the ring opening and scaffold rearrangement of spirocycles in the presence of ferric chloride under ambient conditions. Control experiments shown that this reaction may proceeded through a radical cation mechanism and futher theoretical calculation revealed that the electronic distribution of the radical cation intermediate dominated this oxidative rearrangement instead of dehydrogenation. It is noteworthy that some interesting photophysical properties, including aggregation-induced emission, halochromism, and two-photon fluorescence, were discovered for the azulen-6-one 2a, making them to work as promising functional materials in optical-related fields.

14.
Artigo em Inglês | MEDLINE | ID: mdl-34518753

RESUMO

The worldwide spread of COVID-19 has resulted in an enormous threat to public health, causing global panic, especially older adults suffering severe anxiety due to their vulnerability. With a questionnaire survey on 213 Chinese older adults in April 2020, we examined the role of community resilience in protecting older adults from anxiety during the COVID-19 pandemic, and simultaneously considered the moderating role of trust in local government. The results indicated that community resilience was negatively associated with older adults' anxiety, and this association was weakened for older adults with low trust in local government. This study has implications for intervention designs that combine resilient factors related to communities and local governments to relieve older adults' anxiety during the pandemic. Please refer to the Supplementary Material section to find this article's Community and Social Impact Statement.

15.
Plant Dis ; 2021 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-34524867

RESUMO

Onion (Allium cepa L.) is one of the most cultivated vegetables throughout the world. With an average annual production quantity of 18 million kg in recent 21 years, China is the world's biggest onion producer (Hanci F., 2018). Among them, onion is mainly cultivated in the provinces of Gansu, Shandong, Yunnan, Jiangsu, Zhejiang and Henan. A survey in Gansu province in last several years showed that the incidence of onion bulb rot was 30%-80%. In April 2020, bulbs displayed water-soaked, and then rot symptoms observed during storage in Lanzhou City, Gansu Province, China. The initial symptoms of bulb rot disease were yellowish brown, and produced an abundant exudate in the inner bulb scales when cut. Gradually, symptomatic bulbs became soft, watery and decayed. In severe infections, the onions showed total rot of the bulb. Therefore, we sampled some diseased onions and isolated pathogenic bacteria from the junction of lesion along with healthy parts on Luria-Bertani (LB) medium. Three representative single colonies were obtained on LB medium, and the culture characteristics were raised elevation, mucoid texture, round, and smooth with entire margin, the brown at the beginning and turned yellow later, and scanning electron microscopy (SEM) observations showed that these isolates were short rod-shaped (Fig. 1A). The physiological and biochemical determination revealed that the isolates were positive for yellow pigment, v-p test, growth at 37 ℃, nitrate reduced, catalase, glucose, sucrose, D (-)-salicin, starch hydrolysis, motility, pellicle. On the contrary, they were negative for indole production, methyl red, lactose, gelatin liquefaction, glycerol, gram staining (Gavini et al., 1989; Nabrdalik et al., 2018). Based on these morphological, physiological and biochemical characteristics, three isolates were initially identified as Pantoea agglomerans (Guo et al., 2020). A representative isolate L1 was selected to extract DNA, and the conserved sequences of the pathogen gene were sequenced according to 23S ribosomal RNA (23S rRNA), DNA gyrase subunit B (gyrB), elongation factor G (fusA) (She et al., 2021) housekeeping gene. The sequence alignment of the 23S rRNA gene (P. agglomerans, MZ314289, 930bp) showed that the homology between the strain L1 and P. agglomerans (CP016889) with similarity of 99.54%, and based on the sequence alignment of gyrB (P. agglomerans, MZ337547, 1189bp) and fusA (P. agglomerans, MZ350961, 1037bp) genes, the similarity with P. agglomerans (FJ617386 and MG845872) was 100%. A phylogenetic analysis based on the 23S, gyrB, fusA housekeeping gene sequences was performed by using the neighbor-joining methods in MEGA 7.0 under the p-distance (Kumar et al, 2016), which included P. agglomerans strains AR1a, TH81, L15, ASB05, P. eucalypti strain LMG 24197, P. dispersa strains BJQ0007 and DSM 32899, P. ananatis strains LMG 20103 and AJ13355, P. vagans strains C9-1, LMG24199 and PV989. The phylogenetic distribution generated five primary phylogroups, and strain L1 formed a clade with the other four P. agglomerans strains (Fig. 2). Thus, the strain L1 was identified as P. agglomerans. To satisfy Koch's postulates, ten onions were divided into two groups, five in each group, and needle punctured wound on the surface of each onion. In the experimental group, 400 µL bacterial suspensions were injected with sterile syringe, and the other five onions were injected with the same amount of sterile distilled water as the negative conrol. Inoculated onions were incubated in the greenhouse incubator (28 ℃, humidity > 80%). After 4 days of incubation, all onions inoculated with strain L1 appeared water-soaked, rot symptoms, and no symptoms were observed in the negative control (Fig. 1B). Subsequently, pathogens were re-isolated from inoculated bulbs and identified as P. agglomerans according to molecular identification described above. To the best of our knowledge, this is the first report that the bulb rot disease of stored onion caused by P. agglomerans in China.

16.
Front Plant Sci ; 12: 709545, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34490011

RESUMO

Genomic prediction is a promising approach for accelerating the genetic gain of complex traits in wheat breeding. However, increasing the prediction accuracy (PA) of genomic prediction (GP) models remains a challenge in the successful implementation of this approach. Multivariate models have shown promise when evaluated using diverse panels of unrelated accessions; however, limited information is available on their performance in advanced breeding trials. Here, we used multivariate GP models to predict multiple agronomic traits using 314 advanced and elite breeding lines of winter wheat evaluated in 10 site-year environments. We evaluated a multi-trait (MT) model with two cross-validation schemes representing different breeding scenarios (CV1, prediction of completely unphenotyped lines; and CV2, prediction of partially phenotyped lines for correlated traits). Moreover, extensive data from multi-environment trials (METs) were used to cross-validate a Bayesian multi-trait multi-environment (MTME) model that integrates the analysis of multiple-traits, such as G × E interaction. The MT-CV2 model outperformed all the other models for predicting grain yield with significant improvement in PA over the single-trait (ST-CV1) model. The MTME model performed better for all traits, with average improvement over the ST-CV1 reaching up to 19, 71, 17, 48, and 51% for grain yield, grain protein content, test weight, plant height, and days to heading, respectively. Overall, the empirical analyses elucidate the potential of both the MT-CV2 and MTME models when advanced breeding lines are used as a training population to predict related preliminary breeding lines. Further, we evaluated the practical application of the MTME model in the breeding program to reduce phenotyping cost using a sparse testing design. This showed that complementing METs with GP can substantially enhance resource efficiency. Our results demonstrate that multivariate GS models have a great potential in implementing GS in breeding programs.

17.
Plant Dis ; 2021 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-34494867

RESUMO

The yields of edible rhizome from the cultivation of the perennial hydrophyte lotus (Nelumbo nucifera) can be severely reduced by rhizome rot disease caused by Fusarium species. There is a lack of rapid field-applicable methods for detection of these pathogens on lotus plants displaying symptoms of rhizome-rot. Fusarium commune (91%) and Fusarium oxysporum (9%) were identified at different frequencies from lotus samples showing symptoms of rhizome-rot. As these two species can cause different severity of disease and their morphology is very similar, molecular-diagnostic based methods to detect these two species were developed. Based on the comparison of the mitochondrial genome of the two species, three specific DNA loci targets were found. The designed primer sets for conventional PCR, qPCR and loop-mediated isothermal amplification (LAMP) precisely distinguished the above two species when isolated from lotus and other plants. The LAMP detection limits were 10 pg/µl and 1 pg/µl of total DNA for F. commune and F. oxysporum, respectively. We also carried out field-mimicked experiments on lotus seedlings and rhizomes (including inoculated samples and field diseased samples), and the results indicated that the LAMP primer sets and the supporting portable methods are suitable for the rapid diagnosis of the lotus disease in the field. The LAMP-based detection method will aid in the rapid identification of whether F. oxysporum or F. commune are infecting lotus plants with symptoms of rhizome-rot, and can facilitate efficient pesticide use and prevent the disease spread through vegetative propagation of Fusarium-infected lotus rhizomes.

18.
Front Plant Sci ; 12: 694229, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34539690

RESUMO

Cryopreservation is one of the key technologies for the mass propagation of conifers via somatic embryogenesis. Cryotolerance and embryogenecity of conifer somatic embryos (SEs) could be affected by different temperature treatments, for which the underlying mechanisms were unknown. In this study, the developing SEs of Picea glauca obtained their cryotolerance with a survival rate of 100% when cultured on maturation medium at either 23°C for 4 weeks or 4°C for 10 weeks. However, only the embryos that underwent 4°C acclimation remained high embryogenicity, i.e., 91.7% based on cryovials or 29.3% on the plant tissue. Analysis of differentially expressed genes (DEGs) revealed that both 23 and 4°C treatments led to drastic changes in the gene expression, i.e., 21,621 and 14,906 genes, respectively, and the general increase in many oligosaccharides and flavonoids, in addition to the content change of proline (1.9- and 2.3-fold at 23 or 4°C) and gallic acid (6,963- and 22,053-fold). There were 249 significantly different metabolites between the samples of 23 and 4°C treatments and the changing trend of the sorbitol, fatty acids, and monosaccharides differed between these samples. During 4°C-acclimation, the metabolites of the arginine biosynthesis pathway increased between 2.4- and 8.1-fold, and the expression of antioxidant genes was up-regulated significantly. At 4°C, the up-regulated genes were for germ-like proteins, instead of seed storage proteins at 23°C. Concentrations of abscisic acid and jasmonic acid increased up to 2- and 1.5-fold, respectively, in the cold-acclimated embryos. After 10 weeks at 4°C, the embryos stayed at pre-cotyledonary stage with 17.1% less DNA methylation and fewer storage substances than those at 23°C for 4 weeks, which developed cotyledons. This research provides new insights into mechanisms underlying the response of SEs to different culture temperatures and benefits method development for germplasm conservation in conifers.

19.
ACM BCB ; 20212021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34414397

RESUMO

The rapid adoption of electronic health records (EHRs) systems has made clinical data available in electronic format for research and for many downstream applications. Electronic screening of potentially eligible patients using these clinical databases for clinical trials is a critical need to improve trial recruitment efficiency. Nevertheless, manually translating free-text eligibility criteria into database queries is labor intensive and inefficient. To facilitate automated screening, free-text eligibility criteria must be structured and coded into a computable format using controlled vocabularies. Named entity recognition (NER) is thus an important first step. In this study, we evaluate 4 state-of-the-art transformer-based NER models on two publicly available annotated corpora of eligibility criteria released by Columbia University (i.e., the Chia data) and Facebook Research (i.e.the FRD data). Four transformer-based models (i.e., BERT, ALBERT, RoBERTa, and ELECTRA) pretrained with general English domain corpora vs. those pretrained with PubMed citations, clinical notes from the MIMIC-III dataset and eligibility criteria extracted from all the clinical trials on ClinicalTrials.gov were compared. Experimental results show that RoBERTa pretrained with MIMIC-III clinical notes and eligibility criteria yielded the highest strict and relaxed F-scores in both the Chia data (i.e., 0.658/0.798) and the FRD data (i.e., 0.785/0.916). With promising NER results, further investigations on building a reliable natural language processing (NLP)-assisted pipeline for automated electronic screening are needed.

20.
PLoS Genet ; 17(8): e1009689, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34383745

RESUMO

Elucidating the transcriptional regulatory networks that underlie growth and development requires robust ways to define the complete set of transcription factor (TF) binding sites. Although TF-binding sites are known to be generally located within accessible chromatin regions (ACRs), pinpointing these DNA regulatory elements globally remains challenging. Current approaches primarily identify binding sites for a single TF (e.g. ChIP-seq), or globally detect ACRs but lack the resolution to consistently define TF-binding sites (e.g. DNAse-seq, ATAC-seq). To address this challenge, we developed MNase-defined cistrome-Occupancy Analysis (MOA-seq), a high-resolution (< 30 bp), high-throughput, and genome-wide strategy to globally identify putative TF-binding sites within ACRs. We used MOA-seq on developing maize ears as a proof of concept, able to define a cistrome of 145,000 MOA footprints (MFs). While a substantial majority (76%) of the known ATAC-seq ACRs intersected with the MFs, only a minority of MFs overlapped with the ATAC peaks, indicating that the majority of MFs were novel and not detected by ATAC-seq. MFs were associated with promoters and significantly enriched for TF-binding and long-range chromatin interaction sites, including for the well-characterized FASCIATED EAR4, KNOTTED1, and TEOSINTE BRANCHED1. Importantly, the MOA-seq strategy improved the spatial resolution of TF-binding prediction and allowed us to identify 215 motif families collectively distributed over more than 100,000 non-overlapping, putatively-occupied binding sites across the genome. Our study presents a simple, efficient, and high-resolution approach to identify putative TF footprints and binding motifs genome-wide, to ultimately define a native cistrome atlas.


Assuntos
Pegada de DNA/métodos , Regiões Promotoras Genéticas , Fatores de Transcrição/metabolismo , Zea mays/genética , Sítios de Ligação , Sequenciamento de Cromatina por Imunoprecipitação , Sequenciamento de Nucleotídeos em Larga Escala , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Elementos Reguladores de Transcrição , Sequenciamento Completo do Genoma
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