Publications by authors named "Delin Li"

33 Publications

Natural variations in the P-type ATPase heavy metal transporter ZmHMA3 controlling cadmium accumulation in maize grains.

J Exp Bot 2021 Jun 3. Epub 2021 Jun 3.

Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.

Cadmium (Cd) accumulation in maize grains is detrimental to human health. Developing maize varieties with low-Cd contents is important for maize grains safe consumption. However, the key genes controlling maize grain Cd accumulation have not been cloned. Here, we identified one major locus for maize grain Cd accumulation (qCd1) using a genome-wide association study (GWAS) and bulked segregant RNA-seq analysis with a biparental segregating population of Jing724 (low-Cd line) and Mo17 (high-Cd line). The candidate gene ZmHMA3 was identified by fine mapping, which encodes a tonoplast-localized heavy metal P-type ATPase transporter. An EMS mutant analysis and an allelism test confirmed that ZmHMA3 influences maize grain Cd accumulation. A transposon in intron 1 of ZmHMA3 is responsible for the abnormal amino acid sequence in Mo17. Based on the natural sequence variations in ZmHMA3 gene of diverse maize lines, four PCR-based molecular markers were developed, which were successfully used to distinguish five haplotypes with different grain Cd contents in the GWAS panel and to predict grain Cd content levels of widely used maize inbred lines and hybrids. These molecular markers can be used to breed elite maize varieties with low grain Cd contents.
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http://dx.doi.org/10.1093/jxb/erab254DOI Listing
June 2021

Hydrogen-Bonded Organic Framework Microlasers with Conformation-Induced Color-Tunable Output.

ACS Appl Mater Interfaces 2021 Jun 11;13(24):28662-28667. Epub 2021 Jun 11.

Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.

Porous organic frameworks have emerged as the promising platforms to construct tunable microlasers. Most of these microlasers are achieved from metal-organic frameworks via meticulously accommodating the laser dyes with the sacrifice of the pore space, yet they often suffer from the obstacles of either relatively limited gain concentration or sophisticated fabrication techniques. Herein, we reported on the first hydrogen-bonded organic framework (HOF) microlasers with color-tunable performance based on conformation-dependent stimulated emissions. Two types of HOF microcrystals with the same gain lumnogen as the building block were synthesized via a temperature-controlled self-assembly method. The distinct frameworks offer different conformations of the gain building block, which lead to great impacts on their conjugation degrees and excited-state processes, resulting in remarkably distinct emission colors (blue and green). Accordingly, blue/green-color lasing actions were achieved in these two types of HOFs based on well-faceted assembled wire-like cavities. These results offer a deep insight on the exploitation of HOF-based miniaturized lasers with desired nanophotonics performances.
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http://dx.doi.org/10.1021/acsami.1c06312DOI Listing
June 2021

Clinical Features and Outcomes of Adrenal Cavernous Hemangioma: A Study of 8 Cases from a Single Center.

Int J Endocrinol 2021 28;2021:5549925. Epub 2021 Apr 28.

Department of Pathology, The First Affliated Hospital of GuangXi Medical University, Nanning, GuangXi, China.

Background: Cavernous hemangioma is a rare benign tumor that develops from the adrenal glands. In this study, we present our experience with patients with adrenal cavernous hemangiomas (ACH) in a Chinese population.

Methods: Demographic, diagnostic, surgical, and pathological findings in patients at a single institution who were adrenalectomized as a result of ACH were retrospectively reviewed.

Results: Among 601 patients who underwent adrenalectomy, 8 (1.33%; 5 men, 3 women) cases were diagnosed with ACH between January 1, 1998, and December 31, 2018, in a single institution. The mean age was 53.25 ± 11.9 years (range, 35-67 years). Four (50%) were asymptomatic, and three (37.5%) complained of abdominal or flank discomfort. Preoperative computed tomography (CT) revealed ACH in 3 (37.5%) cases. Well-defined borders and heterogeneous enhancement with characteristic progressive partial filling-in were characteristic CT features of ACH (tumor size>3 cm). The mean tumor size was 5.16 ± 3.4 cm (range, 1.5-11 cm). No recurrence occurred during a median follow-up period of 38.37 months (range, 8-60 months).

Conclusions: ACH was asymptomatic in most cases, and diagnosis could be challenging. Adrenalectomy is a safe treatment modality for ACH, and it ensures favorable outcomes.
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http://dx.doi.org/10.1155/2021/5549925DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8099531PMC
April 2021

Clinical features and outcomes of adrenal schwannoma: a study of 13 cases from a single centre.

Endocr Connect 2021 May 19;10(5):543-549. Epub 2021 May 19.

Department of Urology, The First Affiliated Hospital of GuangXi Medical University, Nanning China.

Background: Adrenal schwannomas (AS) are extremely rare neoplasms. This study shares our experience regarding the diagnosis and operative management of AS.

Methods: Clinical details, radiologic, laboratory, and pathologic findings as well as follow-up data were analysed retrospectively for 13 AS patients who accepted surgery at a tertiary referral hospital in China between 1 January 1996, and 31 December 2017.

Results: The mean age of the patients at diagnosis was 44.7 ± 13.7 years (range 19-62 years; male: female ratio, 1:1.16), of whom seven patients had unilateral AS on the right side, and the remaining six on the left side. None of the cases were hormonally active. None of the 13 cases were diagnosed as AS by CT imaging before the operation. Among the patients, ten were asymptomatic. The mean preoperative size was 7.1 ± 3.2 cm (range 1.6-12.6 cm). All patients underwent surgery, with open adrenalectomy in five patients and laparoscopy in eight patients. The mean tumor size on pathologic examination was 6.8 ± 3.0 cm (range 3.0-11.7 cm). The surgical specimens were confirmed by pathological examination. During a median follow-up of 60.8 ± 17.7 months, no patients showed recurrence or metastasis.

Conclusion: The preoperative diagnosis of AS remains difficult despite the advances in imaging examinations. After complete resection, the prognosis of AS is excellent.
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http://dx.doi.org/10.1530/EC-21-0062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8183624PMC
May 2021

TWAS results are complementary to and less affected by linkage disequilibrium than GWAS.

Plant Physiol 2021 Apr 6. Epub 2021 Apr 6.

Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China.

A genome-wide association study (GWAS) is used to identify genetic markers associated with phenotypic variation. In contrast, a transcriptome-wide association study (TWAS) detects associations between gene expression levels and phenotypic variation. It has previously been shown that in the cross-pollinated species, maize (Zea mays), GWAS and TWAS identify complementary sets of trait-associated genes, many of which exhibit characteristics of true positives. Here, we extend this conclusion to the self-pollinated species, Arabidopsis thaliana and soybean (Glycine max). Linkage disequilibrium (LD) can result in the identification, via GWAS, of false-positive associations. In all three analyzed plant species, most trait-associated genes identified via TWAS are well separated physically from other candidate genes. Hence, TWAS is less affected by LD than is GWAS, demonstrating that TWAS is particularly well suited for association studies in genomes with slow rates of LD decay, such as soybean. TWAS is reasonably robust to the plant organs/tissues used to determine expression levels. In summary, this study confirms that TWAS is a promising approach for accurate gene-level association mapping in plants that is complementary to GWAS, and established that TWAS can exhibit substantial advantages relative to GWAS in species with slow rates of LD decay.
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http://dx.doi.org/10.1093/plphys/kiab161DOI Listing
April 2021

MEMS-on-fiber sensor combining silicon diaphragm and supporting beams for on-line partial discharges monitoring.

Opt Express 2020 Sep;28(20):29368-29376

Fiber optic extrinsic Fabry-Perot interferometric (EFPI) sensors are ideal candidates for on-line partial discharges (PDs) monitoring due to their inherent advantages, such as immunity to electromagnetic interference (EMI), highly compact sensing probes, and remote signal transmission. However, up to date, the design and fabrication of high-performance sensing diaphragms still remain challenging, and most of the reported diaphragms utilize circular structures with the peripheral sidewalls completely fixed. Herein, a novel EFPI ultrasonic sensor for on-line PDs monitoring is demonstrated. The proposed sensing diaphragm combines a silicon beam-supported diaphragm and a fixed boundary ring with a thickness of 5 µm, which was optimized through the multi-objective genetic algorithm (MOGA) revealing its high design flexibility and manufactured by using the microelectromechanical systems (MEMS) processing technology on a silicon-on-insulator (SOI) wafer. Compared with the circular and beam-supported diaphragm, the developed structure exhibits a higher sensitivity. The testing results show that the developed sensor owns the sensitivity and noise-limited minimum detectable ultrasonic pressure (MDUP) of -10 dB re. 1V/Pa and 63 µPa/sqrt(Hz) at its designed resonant frequency, respectively. Finally, the sensor's ability to detect PDs is validated in a temporary built PDs experimental environment, further proving its great potential to perform the on-line PDs monitoring.
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http://dx.doi.org/10.1364/OE.405249DOI Listing
September 2020

Genome-wide analyses reveal footprints of divergent selection and popping-related traits in CIMMYT's maize inbred lines.

J Exp Bot 2021 02;72(4):1307-1320

Institute of Crop Sciences, The National Key Facility for Crop Gene Resources and Genetic Improvement and CIMMYT China office, Chinese Academy of Agricultural Sciences, Beijing, China.

Popcorn (Zea mays L. var. Everta) is the most ancient type of cultivated maize. However, there is little known about the genetics of popping-related traits based on genotyping-by-sequencing (GBS) technology. Here, we characterized the phenotypic variation for seven popping-related traits in maize kernels among 526 CIMMYT inbred lines (CMLs). In total, 155 083 high-quality single nucleotide polymorphism (SNP) markers were identified by a GBS approach. Several trait-associated loci were detected by genome-wide association study for color, popping expansion volume, shape, pericarp, flotation index, floury/vitreous, and protein content, explaining a majority of the observed phenotypic variance, and these were validated by a diverse panel comprising 764 tropical landrace accessions. Sixty two of the identified loci were recognized to have undergone selection. On average, there was a 55.27% frequency for alleles that promote popping in CMLs. Our work not only pinpoints previously unknown loci for popping-related traits, but also reveals that many of these loci have undergone selection. Beyond establishing a new benchmark for the genetics of popcorn, our study provides a foundation for gene discovery and breeding. It also presents evidence to investigate the role of a gradual loss of popping ability as a by-product of diversification of culinary uses throughout the evolution of teosinte-to-modern maize.
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http://dx.doi.org/10.1093/jxb/eraa480DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7904155PMC
February 2021

Maize Defective Kernel605 Encodes a Canonical DYW-Type PPR Protein that Edits a Conserved Site of nad1 and Is Essential for Seed Nutritional Quality.

Plant Cell Physiol 2020 Dec;61(11):1954-1966

Institute of Crop Sciences, Chinese Academy of Agricultural iences, Beijing 100081, China.

Pentatricopeptide repeat (PPR) proteins involved in mitochondrial RNA cytidine (C)-to-uridine (U) editing mostly result in stagnant embryo and endosperm development upon loss of function. However, less is known about PPRs that are involved in farinaceous endosperm formation and maize quality. Here, we cloned a maize DYW-type PPR Defective Kernel605 (Dek605). Mutation of Dek605 delayed seed and seedling development. Mitochondrial transcript analysis of dek605 revealed that loss of DEK605 impaired C-to-U editing at the nad1-608 site and fails to alter Ser203 to Phe203 in NAD1 (dehydrogenase complex I), disrupting complex I assembly and reducing NADH dehydrogenase activity. Meanwhile, complexes III and IV in the cytochrome pathway, as well as AOX2 in the alternative respiratory pathway, are dramatically increased. Interestingly, the dek605 mutation resulted in opaque endosperm and increased levels of the free amino acids alanine, aspartic acid and phenylalanine. The down- and upregulated genes mainly involved in stress response-related and seed dormancy-related pathways, respectively, were observed after transcriptome analysis of dek605 at 12 d after pollination. Collectively, these results indicate that Dek605 specifically affects the single nad1-608 site and is required for normal seed development and resulted in nutritional quality relevant amino acid accumulation.
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http://dx.doi.org/10.1093/pcp/pcaa110DOI Listing
December 2020

MEMS-on-fiber ultrasonic sensor with two resonant frequencies for partial discharges detection.

Opt Express 2020 Jun;28(12):18431-18439

A novel fiber optic extrinsic Fabry-Perot interferometric (EFPI) ultrasonic sensor with two resonant frequencies for detecting the partial discharges (PDs) in switchgear is demonstrated. The key sensing element consists of two 5-µm-thickness and beam-supported silicon diaphragms, whose natural frequencies are designed differently to enable the sensor to achieve the resonant responses at two different frequencies, thus obtaining a broadened frequency response. The sensing element is fabricated by employing the microelectromechanical systems (MEMS) technology on a silicon-on-insulator (SOI) wafer. The experimental results show that the sensor possesses two resonant frequencies of 31 kHz and 63 kHz, and obviously, shows a highly sensitive frequency response over a broader range compared with the approach composed of a single sensing diaphragm with only one resonant frequency. The noise-limited minimum detectable ultrasonic pressure (MDUP) reaches 251 µPa/[email protected] 31 kHz and 316 µPa/[email protected] 63 kHz, respectively.
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http://dx.doi.org/10.1364/OE.391242DOI Listing
June 2020

MicroRNA-377 Alleviates Myocardial Injury Induced by Hypoxia/Reoxygenation via Downregulating LILRB2 Expression.

Dose Response 2020 Apr-Jun;18(2):1559325820936124. Epub 2020 Jun 30.

Department of Cardiology, Guihang Guiyang Hospital, Guizhou, China.

Background: miR-377 is closely related to myocardial regeneration. miR-377-adjusted mesenchymal stem cells abducted ischemic cardiac angiogenesis. Nevertheless, there were rarely reports about the impact of miR-377 on myocardial ischemia injury. The purpose of this work is that whether miR-377 can protect against myocardial injury caused by hypoxia/reoxygenation (H/R).

Methods: Gene expression omnibus database (http://www.ncbi.nlm.nih.gov/geo/; no. GSE53211) was utilized to study the differential expression of miR-377 in patients with an acute ST-segment elevation myocardial infarction and healthy controls. The luciferase activity was determined utilizing the dual-luciferase reporter system. Quantitative real-time polymerase chain reaction and Western blotting were used to measure the messenger RNA and protein level.

Results: Low expression of miR-377 and high expression of leukocyte immunoglobulin-like receptor B2 (LILRB2) were identified in patients with myocardial infarction from analyzing the Gene Expression Omnibus data set. Besides, miR-377 expression was downregulated in cardiomyocyte exposed to H/R. Additionally, overexpression of miR-377 could visibly improve cardiomyocyte injury by regulating cell activity and apoptosis.

Conclusions: In short, our findings suggested that miR-377/LILRB2 might regard as a hopeful therapeutic target for myocardial ischemic.
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http://dx.doi.org/10.1177/1559325820936124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7328223PMC
June 2020

A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2.

Science 2020 06 13;368(6496):1274-1278. Epub 2020 May 13.

Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China.

Neutralizing antibodies could potentially be used as antivirals against the coronavirus disease 2019 (COVID-19) pandemic. Here, we report isolation of four human-origin monoclonal antibodies from a convalescent patient, all of which display neutralization abilities. The antibodies B38 and H4 block binding between the spike glycoprotein receptor binding domain (RBD) of the virus and the cellular receptor angiotensin-converting enzyme 2 (ACE2). A competition assay indicated different epitopes on the RBD for these two antibodies, making them a potentially promising virus-targeting monoclonal antibody pair for avoiding immune escape in future clinical applications. Moreover, a therapeutic study in a mouse model validated that these antibodies can reduce virus titers in infected lungs. The RBD-B38 complex structure revealed that most residues on the epitope overlap with the RBD-ACE2 binding interface, explaining the blocking effect and neutralizing capacity. Our results highlight the promise of antibody-based therapeutics and provide a structural basis for rational vaccine design.
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http://dx.doi.org/10.1126/science.abc2241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223722PMC
June 2020

Plasma IP-10 and MCP-3 levels are highly associated with disease severity and predict the progression of COVID-19.

J Allergy Clin Immunol 2020 Jul 29;146(1):119-127.e4. Epub 2020 Apr 29.

Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China. Electronic address:

Background: The outbreak of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 was first reported in Wuhan, December 2019, and continuously poses a serious threat to public health, highlighting the urgent need of identifying biomarkers for disease severity and progression.

Objective: We sought to identify biomarkers for disease severity and progression of COVID-19.

Methods: Forty-eight cytokines in the plasma samples from 50 COVID-19 cases including 11 critically ill, 25 severe, and 14 moderate patients were measured and analyzed in combination with clinical data.

Results: Levels of 14 cytokines were found to be significantly elevated in COVID-19 cases and showed different expression profiles in patients with different disease severity. Moreover, expression levels of IFN-γ-induced protein 10, monocyte chemotactic protein-3, hepatocyte growth factor, monokine-induced gamma IFN, and macrophage inflammatory protein 1 alpha, which were shown to be highly associated with disease severity during disease progression, were remarkably higher in critically ill patients, followed by severe and then the moderate patients. Serial detection of the 5 cytokines in 16 cases showed that continuously high levels were associated with deteriorated progression of disease and fatal outcome. Furthermore, IFN-γ-induced protein 10 and monocyte chemotactic protein-3 were excellent predictors for the progression of COVID-19, and the combination of the 2 cytokines showed the biggest area under the curve of the receiver-operating characteristics calculations with a value of 0.99.

Conclusions: In this study, we report biomarkers that are highly associated with disease severity and progression of COVID-19. These findings add to our understanding of the immunopathologic mechanisms of severe acute respiratory syndrome coronavirus 2 infection, and provide potential therapeutic targets and strategies.
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http://dx.doi.org/10.1016/j.jaci.2020.04.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7189843PMC
July 2020

Treatment of 5 Critically Ill Patients With COVID-19 With Convalescent Plasma.

JAMA 2020 04;323(16):1582-1589

Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China.

Importance: Coronavirus disease 2019 (COVID-19) is a pandemic with no specific therapeutic agents and substantial mortality. It is critical to find new treatments.

Objective: To determine whether convalescent plasma transfusion may be beneficial in the treatment of critically ill patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.

Design, Setting, And Participants: Case series of 5 critically ill patients with laboratory-confirmed COVID-19 and acute respiratory distress syndrome (ARDS) who met the following criteria: severe pneumonia with rapid progression and continuously high viral load despite antiviral treatment; Pao2/Fio2 <300; and mechanical ventilation. All 5 were treated with convalescent plasma transfusion. The study was conducted at the infectious disease department, Shenzhen Third People's Hospital in Shenzhen, China, from January 20, 2020, to March 25, 2020; final date of follow-up was March 25, 2020. Clinical outcomes were compared before and after convalescent plasma transfusion.

Exposures: Patients received transfusion with convalescent plasma with a SARS-CoV-2-specific antibody (IgG) binding titer greater than 1:1000 (end point dilution titer, by enzyme-linked immunosorbent assay [ELISA]) and a neutralization titer greater than 40 (end point dilution titer) that had been obtained from 5 patients who recovered from COVID-19. Convalescent plasma was administered between 10 and 22 days after admission.

Main Outcomes And Measures: Changes of body temperature, Sequential Organ Failure Assessment (SOFA) score (range 0-24, with higher scores indicating more severe illness), Pao2/Fio2, viral load, serum antibody titer, routine blood biochemical index, ARDS, and ventilatory and extracorporeal membrane oxygenation (ECMO) supports before and after convalescent plasma transfusion.

Results: All 5 patients (age range, 36-65 years; 2 women) were receiving mechanical ventilation at the time of treatment and all had received antiviral agents and methylprednisolone. Following plasma transfusion, body temperature normalized within 3 days in 4 of 5 patients, the SOFA score decreased, and Pao2/Fio2 increased within 12 days (range, 172-276 before and 284-366 after). Viral loads also decreased and became negative within 12 days after the transfusion, and SARS-CoV-2-specific ELISA and neutralizing antibody titers increased following the transfusion (range, 40-60 before and 80-320 on day 7). ARDS resolved in 4 patients at 12 days after transfusion, and 3 patients were weaned from mechanical ventilation within 2 weeks of treatment. Of the 5 patients, 3 have been discharged from the hospital (length of stay: 53, 51, and 55 days), and 2 are in stable condition at 37 days after transfusion.

Conclusions And Relevance: In this preliminary uncontrolled case series of 5 critically ill patients with COVID-19 and ARDS, administration of convalescent plasma containing neutralizing antibody was followed by improvement in their clinical status. The limited sample size and study design preclude a definitive statement about the potential effectiveness of this treatment, and these observations require evaluation in clinical trials.
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http://dx.doi.org/10.1001/jama.2020.4783DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101507PMC
April 2020

Identifying loci with breeding potential across temperate and tropical adaptation via EigenGWAS and EnvGWAS.

Mol Ecol 2019 08 18;28(15):3544-3560. Epub 2019 Aug 18.

Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.

Understanding the genomic basis of adaptation in maize is important for gene discovery and the improvement of breeding germplasm, but much remains a mystery in spite of significant population genetics and archaeological research. Identifying the signals underpinning adaptation are challenging as adaptation often coincided with genetic drift, and the base genomic diversity of the species in massive. In this study, tGBS technology was used to genotype 1,143 diverse maize accessions including landraces collected from 20 countries and elite breeding lines of tropical lowland, highland, subtropical/midaltitude and temperate ecological zones. Based on 355,442 high-quality single nucleotide polymorphisms, 13 genomic regions were detected as being under selection using the bottom-up searching strategy, EigenGWAS. Of the 13 selection regions, 10 were first reported, two were associated with environmental parameters via EnvGWAS, and 146 genes were enriched. Combining large-scale genomic and ecological data in this diverse maize panel, our study supports a polygenic adaptation model of maize and offers a framework to enhance our understanding of both the mechanistic basis and the evolutionary consequences of maize domestication and adaptation. The regions identified here are promising candidates for further, targeted exploration to identify beneficial alleles and haplotypes for deployment in maize breeding.
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http://dx.doi.org/10.1111/mec.15169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6851670PMC
August 2019

Identification of loci controlling adaptation in Chinese soya bean landraces via a combination of conventional and bioclimatic GWAS.

Plant Biotechnol J 2020 02 24;18(2):389-401. Epub 2019 Jul 24.

The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.

Landraces often contain genetic diversity that has been lost in modern cultivars, including alleles that confer enhanced local adaptation. To comprehensively identify loci associated with adaptive traits in soya bean landraces, for example flowering time, a population of 1938 diverse landraces and 97 accessions of the wild progenitor of cultivated soya bean, Glycine soja was genotyped using tGBS . Based on 99 085 high-quality SNPs, landraces were classified into three sub-populations which exhibit geographical genetic differentiation. Clustering was inferred from STRUCTURE, principal component analyses and neighbour-joining tree analyses. Using phenotypic data collected at two locations separated by 10 degrees of latitude, 17 trait-associated SNPs (TASs) for flowering time were identified, including a stable locus Chr12:5914898 and previously undetected candidate QTL/genes for flowering time in the vicinity of the previously cloned flowering genes, E1 and E2. Using passport data associated with the collection sites of the landraces, 27 SNPs associated with adaptation to three bioclimatic variables (temperature, daylength, and precipitation) were identified. A series of candidate flowering genes were detected within linkage disequilibrium (LD) blocks surrounding 12 bioclimatic TASs. Nine of these TASs exhibit significant differences in flowering time between alleles within one or more of the three individual sub-populations. Signals of selection during domestication and/or subsequent landrace diversification and adaptation were detected at 38 of the 44 flowering and bioclimatic TASs. Hence, this study lays the groundwork to begin breeding for novel environments predicted to arise following global climate change.
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http://dx.doi.org/10.1111/pbi.13206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6953199PMC
February 2020

Enzymatic decolorization of melanoidins from molasses wastewater by immobilized keratinase.

Bioresour Technol 2019 May 10;280:165-172. Epub 2019 Feb 10.

Yongxin Sugar Industry Company, Laibin 546100, PR China.

The aim of this work was to study the ability of commercial immobilized hydrolases in the decolorization of molasses wastewater. Commercial immobilized keratinase obtained the highest decolorization yield (86.6-91.1%) among all of commercial immobilized enzymes tested. Immobilized keratinase had the potential to replace immobilized oxidoreductase to decolorize molasses wastewater. Keratinase from Meiothermus taiwanensis WR-220 (KMT) immobilized on modified bagasse cellulose obtained a decolorization yield of 84.7-90.2%. It removed 60.2-65.6% of colorants and 61.4-69.8% of chemical oxygen demand (COD) for 5 days continuously. Notably, the treatment cost was less than 0.15 dollar per ton. Immobilized KMT-wt had similar performance with commercial immobilized keratinase in bleaching molasses wastewater. Importantly, it was more economic. Finally, the results confirmed that additional reaction catalyzing the unsaturated bonds to destroy the conjugated system by keratinase, weakening the chromogenic group of melanoidins. Accordingly, this work is meaningful to the industrial decolorization of molasses wastewater.
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http://dx.doi.org/10.1016/j.biortech.2019.02.049DOI Listing
May 2019

The genome of broomcorn millet.

Nat Commun 2019 01 25;10(1):436. Epub 2019 Jan 25.

Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China.

Broomcorn millet (Panicum miliaceum L.) is the most water-efficient cereal and one of the earliest domesticated plants. Here we report its high-quality, chromosome-scale genome assembly using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. Phylogenetic analyses reveal two sets of homologous chromosomes that may have merged ~5.6 million years ago, both of which exhibit strong synteny with other grass species. Broomcorn millet contains 55,930 protein-coding genes and 339 microRNA genes. We find Paniceae-specific expansion in several subfamilies of the BTB (broad complex/tramtrack/bric-a-brac) subunit of ubiquitin E3 ligases, suggesting enhanced regulation of protein dynamics may have contributed to the evolution of broomcorn millet. In addition, we identify the coexistence of all three C subtypes of carbon fixation candidate genes. The genome sequence is a valuable resource for breeders and will provide the foundation for studying the exceptional stress tolerance as well as C biology.
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http://dx.doi.org/10.1038/s41467-019-08409-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347628PMC
January 2019

Low-Cost, High-Performance Fiber Optic Fabry⁻Perot Sensor for Ultrasonic Wave Detection.

Sensors (Basel) 2019 Jan 19;19(2). Epub 2019 Jan 19.

Key Laboratory of Micro/Nano Systems for Aerospace (Ministry of Education), Northwestern Polytechnical University, Xi'an 710072, China.

This study describes a novel fiber optic extrinsic Fabry⁻Perot interferometric (EFPI) ultrasonic sensor comprising a low-cost and high-performance silicon diaphragm. A vibrating diaphragm, 5 μm thick, was fabricated by using the Microelectromechanical Systems (MEMS) processing technology on a silicon-on-insulator (SOI) wafer. The Fabry⁻Perot (FP) cavity length was solely determined during the manufacturing process of the diaphragm by defining a specific stepped hole on the handling layer of the SOI wafer, which made the assembly of the sensor easier. In addition, the use of cheap and commercially available components and MEMS processing technology in the development of the sensing system, limited the cost of the sensor. The experimental tests showed that the minimum detectable ultrasonic pressure was 1.5 mPa/sqrt(Hz) ⁻0.625 mPa/sqrt(Hz) between 20 kHz and 40 kHz. As a result, this sensor has the potential to successfully detect weak ultrasonic signals.
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http://dx.doi.org/10.3390/s19020406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6359033PMC
January 2019

Exploiting the Genomic Diversity of Rice ( L.): SNP-Typing in 11 Early-Backcross Introgression-Breeding Populations.

Front Plant Sci 2018 22;9:849. Epub 2018 Jun 22.

National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.

This study demonstrates genotyping-by-sequencing-based single-nucleotide polymorphism (SNP)-typing in 11 early-backcross introgression populations of rice (at BCF), comprising a set of 564 diverse introgression lines and 12 parents. Sequencing using 10 Ion Proton runs generated a total of ∼943.4 million raw reads, out of which ∼881.6 million reads remained after trimming for low-quality bases. After alignment, 794,297 polymorphic SNPs were identified, and filtering resulted in LMD50 SNPs (low missing data, with each SNP, genotyped in at least 50% of the samples) for each sub-population. Every data point was supported by actual sequencing data without any imputation, eliminating imputation-induced errors in SNP calling. Genotyping substantiated the impacts of novel breeding strategy revealing: (a) the donor introgression patterns in ILs were characteristic with variable introgression frequency in different genomic regions, attributed mainly to stringent selection under abiotic stress and (b) considerably lower heterozygosity was observed in ILs. Functional annotation revealed 426 non-synonymous deleterious SNPs present in 102 loci with a range of 1-4 SNPs per locus and 120 novel SNPs. SNP-typing this diversity panel will further assist in the development of markers supporting genomic applications in molecular breeding programs.
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http://dx.doi.org/10.3389/fpls.2018.00849DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6024854PMC
June 2018

Genotype-Corrector: improved genotype calls for genetic mapping in F and RIL populations.

Sci Rep 2018 07 4;8(1):10088. Epub 2018 Jul 4.

Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

F and recombinant inbred lines (RILs) populations are very commonly used in plant genetic mapping studies. Although genome-wide genetic markers like single nucleotide polymorphisms (SNPs) can be readily identified by a wide array of methods, accurate genotype calling remains challenging, especially for heterozygous loci and missing data due to low sequencing coverage per individual. Therefore, we developed Genotype-Corrector, a program that corrects genotype calls and imputes missing data to improve the accuracy of genetic mapping. Genotype-Corrector can be applied in a wide variety of genetic mapping studies that are based on low coverage whole genome sequencing (WGS) or Genotyping-by-Sequencing (GBS) related techniques. Our results show that Genotype-Corrector achieves high accuracy when applied to both synthetic and real genotype data. Compared with using raw or only imputed genotype calls, the linkage groups built by corrected genotype data show much less noise and significant distortions can be corrected. Additionally, Genotype-Corrector compares favorably to the popular imputation software LinkImpute and Beagle in both F and RIL populations. Genotype-Corrector is publicly available on GitHub at https://github.com/freemao/Genotype-Corrector .
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http://dx.doi.org/10.1038/s41598-018-28294-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031647PMC
July 2018

Directional Sensitivity of a MEMS-Based Fiber-Optic Extrinsic Fabry⁻Perot Ultrasonic Sensor for Partial Discharge Detection.

Sensors (Basel) 2018 Jun 20;18(6). Epub 2018 Jun 20.

Key Laboratory of Micro/Nano Systems for Aerospace (Ministry of Education), Northwestern Polytechnical University, Xi'an 710072, China.

Extrinsic Fabry⁻Perot (FP) interferometric sensors are being intensively applied for partial discharge (PD) detection and localization. Previous research work has mainly focused on novel structures and materials to improve the sensitivity and linear response of these sensors. However, the directional response behavior of an FP ultrasonic sensor is also of particular importance in localizing the PD source, which is rarely considered. Here, the directional sensitivity of a microelectromechanical system (MEMS)-based FP ultrasonic sensor with a 5-μm-thick micromechanical vibrating diaphragm is experimentally investigated. Ultrasonic signals from a discharge source with varying incident angles and linear distances are measured and analyzed. The results show that the sensor has a 5.90 dB amplitude fluctuation over a ±60° incident range and an exciting capability to detect weak PD signals from 3 m away due to its high signal⁻noise ratio. The findings are expected to optimize the configuration of a sensor array and accurately localize the PD source.
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http://dx.doi.org/10.3390/s18061975DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022144PMC
June 2018

IMP1 regulates UCA1-mediated cell invasion through facilitating UCA1 decay and decreasing the sponge effect of UCA1 for miR-122-5p.

Breast Cancer Res 2018 04 18;20(1):32. Epub 2018 Apr 18.

Department of Pathophysiology, The Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, 515031, Guangdong Province, China.

Background: Long noncoding RNAs (LncRNAs) represent a class of widespread and diverse endogenous RNAs that can posttranscriptionally regulate gene expression through the interaction with RNA-binding proteins and micro RNAs (miRNAs). Here, we report that in breast carcinoma cells, the insulin-like growth factor 2 messenger RNA binding protein (IMP1) binds to lncRNA urethral carcinoma-associated 1 (UCA1) and suppresses the UCA1-induced invasive phenotype.

Methods: RT-qPCR and RNA sequence assays were used to investigate the expression of UCA1 and miRNAs in breast cancer cells in response to IMP1 expression. The role of IMP1-UCA1 interaction in cell invasion was demonstrated by transwell analysis through loss-of-function and gain-of-function effects. RNA pull-down and RNA binding protein immunoprecipitation (RIP) were performed to confirm the molecular interactions of IMP1-UCA1 and UCA1-miR-122-5p involved in breast cancer cells.

Results: In breast cancer cells, IMP1 interacts with UCA1 via the "ACACCC" motifs within UCA1 and destabilizes UCA1 through the recruitment of CCR4-NOT1 deadenylase complex. Meanwhile, binding of IMP1 prevents the association of miR-122-5p with UCA1, thereby shifting the availability of miR-122-5p from UCA1 to the target mRNAs and reducing the UCA1-mediated cell invasion. Accordingly, either IMP1 silencing or UCA1 overexpression resulted in reduced levels of free miR-122-5p within the cytoplasm, affecting miR-122-5p in regulating its target mRNAs.

Conclusions: Our study provides initial evidence that interaction between IMP1 and UCA1 enhances UCA1 decay and competes for miR-122-5p binding, leading to the liberation of miR-122-5p activity and the reduction of cell invasiveness.
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http://dx.doi.org/10.1186/s13058-018-0959-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5907460PMC
April 2018

Binding of DEAD-box helicase Dhh1 to the 5'-untranslated region of mRNA represses localized translation of in yeast cells.

J Biol Chem 2017 06 27;292(23):9787-9800. Epub 2017 Apr 27.

From the Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515031, China and

Local translation of specific mRNAs is regulated by dynamic changes in their subcellular localization, and these changes are due to complex mechanisms controlling cytoplasmic mRNA transport. The budding yeast is well suited to studying these mechanisms because many of its transcripts are transported from the mother cell to the budding daughter cell. Here, we investigated the translational control of mRNA after transport and localization. We show that although transcripts were translated after they reached the bud tip, some mRNAs were bound by the RNA-binding protein Puf6 and were non-polysomal. We also found that the DEAD-box helicase Dhh1 complexed with the untranslated mRNA and Puf6. Loss of Dhh1 affected local translation of mRNA and resulted in delocalization of transcript in the bud. Forcibly shifting the non-polysomal mRNA into polysomes was associated with Dhh1 dissociation. We further demonstrated that Dhh1 is not recruited to mRNA co-transcriptionally, suggesting that it could bind to mRNA within the cytoplasm. Of note, Dhh1 bound to the 5'-UTR of mRNA and inhibited its translation These results suggest that after localization to the bud tip, a portion of the localized mRNA becomes translationally inactive because of binding of Dhh1 and Puf6 to the 5'- and 3'-UTRs of mRNA.
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http://dx.doi.org/10.1074/jbc.M117.776492DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465500PMC
June 2017

A Novel High-Performance Beam-Supported Membrane Structure with Enhanced Design Flexibility for Partial Discharge Detection.

Sensors (Basel) 2017 Mar 15;17(3). Epub 2017 Mar 15.

Key Laboratory of Micro/Nano Systems for Aerospace (Ministry of Education), Northwestern Polytechnical University, Xi'an 710072, China.

A novel beam-supported membrane (BSM) structure for the fiber optic extrinsic Fabry-Perot interferometer (EFPI) sensors showing an enhanced performance and an improved resistance to the temperature change was proposed for detecting partial discharges (PDs). The fundamental frequency, sensitivity, linear range, and flatness of the BSM structure were investigated by employing the finite element simulations. Compared with the intact membrane (IM) structure commonly used by EFPI sensors, BSM structure provides extra geometrical parameters to define the fundamental frequency when the diameter of the whole membrane and its thickness is determined, resulting in an enhanced design flexibility of the sensor structure. According to the simulation results, it is noted that BSM structure not only shows a much higher sensitivity (increased by almost four times for some cases), and a wider working range of fundamental frequency to choose, but also an improved linear range, making the system development much easier. In addition, BSM structure presents a better flatness than its IM counterpart, providing an increased signal-to-noise ratio (SNR). A further improvement of performance is thought to be possible with a step-forward structural optimization. The BSM structure shows a great potential to design the EFPI sensors, as well as others for detecting the acoustic signals.
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http://dx.doi.org/10.3390/s17030593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5375879PMC
March 2017

Nrf2 inhibits epithelial-mesenchymal transition by suppressing snail expression during pulmonary fibrosis.

Sci Rep 2016 12 16;6:38646. Epub 2016 Dec 16.

The Second Hospital of Dalian Medical University, Dalian, 116023, China.

Epithelial-mesenchymal transition (EMT) is a phenotype conversion that plays a critical role in the development of pulmonary fibrosis (PF). It is known that snail could regulate the progression of EMT. Nuclear factor erythroid 2 related factor 2 (Nrf2), a key regulator of antioxidant defense system, protects cells against oxidative stress. However, it is not known whether Nrf2 regulates snail thereby modulating the development of PF. Here, bleomycin (BLM) was intratracheally injected into both Nrf2-knockout (Nrf2) and wild-type mice to compare the development of PF. Rat type II alveolar epithelial cells (RLE-6TN) were treated with a specific Nrf2 activator sulforaphane, or transfected with Nrf2 and snail siRNAs to determine their effects on transforming growth factor β1 (TGF-β1)-induced EMT. We found that BLM-induced EMT and lung fibrosis were more severe in Nrf2 mice compared to wild-type mice. In vitro, sulforaphane treatment attenuated TGF-β1-induced EMT, accompanied by the down-regulation of snail. Inversely, silencing Nrf2 by siRNA enhanced TGF-β1-induced EMT along with increased expression of snail. Interestingly, when snail was silenced by siRNA, sulforaphane treatment was unable to reduce the progression of EMT in RLE-6TN cells. These findings suggest that Nrf2 attenuates EMT and fibrosis process by regulating the expression of snail in PF.
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http://dx.doi.org/10.1038/srep38646DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5159829PMC
December 2016

Fine genetic mapping of spot blotch resistance gene Sb3 in wheat (Triticum aestivum).

Theor Appl Genet 2016 Mar 8;129(3):577-89. Epub 2016 Jan 8.

State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China.

Key Message: Spot blotch disease resistance gene Sb3 was mapped to a 0.15 centimorgan (cM) genetic interval spanning a 602 kb physical genomic region on chromosome 3BS. Wheat spot blotch disease, caused by B. sorokiniana, is a devastating disease that can cause severe yield losses. Although inoculum levels can be reduced by planting disease-free seed, treatment of plants with fungicides and crop rotation, genetic resistance is likely to be a robust, economical and environmentally friendly tool in the control of spot blotch. The winter wheat line 621-7-1 confers immune resistance against B. sorokiniana. Genetic analysis indicates that the spot blotch resistance of 621-7-1 is controlled by a single dominant gene, provisionally designated Sb3. Bulked segregant analysis (BSA) and simple sequence repeat (SSR) mapping showed that Sb3 is located on chromosome arm 3BS linked with markers Xbarc133 and Xbarc147. Seven and twelve new polymorphic markers were developed from the Chinese Spring 3BS shotgun survey sequence contigs and 3BS reference sequences, respectively. Finally, Sb3 was mapped in a 0.15 cM genetic interval spanning a 602 kb physical genomic region of Chinese Spring chromosome 3BS. The genetic and physical maps of Sb3 provide a framework for map-based cloning and marker-assisted selection (MAS) of the spot blotch resistance.
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http://dx.doi.org/10.1007/s00122-015-2649-zDOI Listing
March 2016

Total glycosides of Yupingfeng protects against bleomycin-induced pulmonary fibrosis in rats associated with reduced high mobility group box 1 activation and epithelial-mesenchymal transition.

Inflamm Res 2015 Dec 28;64(12):953-61. Epub 2015 Sep 28.

School of Pharmacy, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China.

Background: Pulmonary fibrosis (PF) is a fatal inflammatory disease with limited effective strategies. Epithelial-mesenchymal transition (EMT) is a pivotal origin of myofibroblasts that secrete extracellular matrix (ECM) in the development of PF. High mobility group box 1 (HMGB1), one of the mediators of inflammation, has been proved abnormal activation in the pathogenesis of PF.

Aim: The present study was aimed to investigate the potential effects of total glycoside of Yupingfeng (YPF-G), the natural compound extracted from Yupingfeng san, on HMGB1 activation and EMT in bleomycin-induced PF, which was a serious disease of respiratory system.

Methods: The Sprague-Dawley (SD) rat model of PF was duplicated by intratracheal instillation of bleomycin (5 mg kg(-1)). After that, YPF-G (5, 10 mg kg(-1)) and prednisone (5 mg kg(-1)) were separately administered intragastrically, and then the rats were killed at days 14 and 28, respectively. Hematoxylin and eosin and Masson's trichrome staining were performed to assess the histopathologic level of lung tissues, western blotting and the common kits were utilized to investigate the hallmarks molecule expression of ECM and EMT, and the level of HMGB1 in lung tissues and serum.

Results: We found that both dose of YPF-G markedly reduced bleomycin-induced alveolitis and PF in rats. Besides, the levels of HMGB1, laminin, hyaluronic acid, and hydroxyproline were effectively reduced. Meanwhile, the increased protein expression of HMGB1 and the mesenchymal markers including vimentin and alpha-smooth muscle actin, and the decreased protein expression of epithelial marker E-cadherin were dramatically inhibited after YPF-G treatment.

Conclusion: Our results demonstrated that YPF-G could ameliorate bleomycin-induced PF by reducing HMGB1 activation and reversing EMT.
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http://dx.doi.org/10.1007/s00011-015-0878-xDOI Listing
December 2015

Chlorophyll Synthase under Epigenetic Surveillance Is Critical for Vitamin E Synthesis, and Altered Expression Affects Tocopherol Levels in Arabidopsis.

Plant Physiol 2015 Aug 5;168(4):1503-11. Epub 2015 Jun 5.

National Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China (C.Z., W.Z., D.L., Y.Z., E.B.C.);Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture, Wuhan 430070, China (C.Z., W.Z., D.L., Y.Z.); andCenter for Plant Science Innovation and Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588 (C.Z., G.R., R.E.C., M.C., B.Y., E.B.C.)

Chlorophyll synthase catalyzes the final step in chlorophyll biosynthesis: the esterification of chlorophyllide with either geranylgeranyl diphosphate or phytyl diphosphate (PDP). Recent studies have pointed to the involvement of chlorophyll-linked reduction of geranylgeranyl by geranylgeranyl reductase as a major pathway for the synthesis of the PDP precursor of tocopherols. This indirect pathway of PDP synthesis suggests a key role of chlorophyll synthase in tocopherol production to generate the geranylgeranyl-chlorophyll substrate for geranylgeranyl reductase. In this study, contributions of chlorophyll synthase to tocopherol formation in Arabidopsis (Arabidopsis thaliana) were explored by disrupting and altering expression of the corresponding gene CHLOROPHYLL SYNTHASE (CHLSYN; At3g51820). Leaves from the homozygous chlysyn1-1 null mutant were nearly devoid of tocopherols, whereas seeds contained only approximately 25% of wild-type tocopherol levels. Leaves of RNA interference lines with partial suppression of CHLSYN displayed marked reductions in chlorophyll but up to a 2-fold increase in tocopherol concentrations. Cauliflower mosaic virus35S-mediated overexpression of CHLSYN unexpectedly caused a cosuppression phenotype at high frequencies accompanied by strongly reduced chlorophyll content and increased tocopherol levels. This phenotype and the associated detection of CHLSYN-derived small interfering RNAs were reversed with CHLSYN overexpression in rna-directed rna polymerase6 (rdr6), which is defective in RNA-dependent RNA polymerase6, a key enzyme in sense transgene-induced small interfering RNA production. CHLSYN overexpression in rdr6 had little effect on chlorophyll content but resulted in up to a 30% reduction in tocopherol levels in leaves. These findings show that altered CHLSYN expression impacts tocopherol levels and also, show a strong epigenetic surveillance of CHLSYN to control chlorophyll and tocopherol synthesis.
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http://dx.doi.org/10.1104/pp.15.00594DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528762PMC
August 2015

Total extract of Yupingfeng attenuates bleomycin-induced pulmonary fibrosis in rats.

Phytomedicine 2015 Jan 20;22(1):111-9. Epub 2014 Nov 20.

Pharmaceutical Preparation Section (Third-Grade Pharmaceutical Chemistry Laboratory of State Administration of Traditional Chinese Medicine (TCM-2009-202)), The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China. Electronic address:

Yupingfeng is a Chinese herbal compound used efficaciously to treat respiratory tract diseases. Total glucosides of Yupingfeng have been proven effective in anti-inflammation and immunoregulation. Nevertheless, the role of total extract of Yupingfeng (YTE) in pulmonary fibrosis (PF), a severe lung disease with no substantial therapies, remains unknown. Present study was conducted to elucidate the anti-fibrotic activity of YTE. The rat PF model was induced by intratracheal administration of bleomycin (BLM, 5 mg/kg), and YTE (12 mg/kg/d) was gavaged from the second day. At 14 and 28 days, the lungs were harvested and stained with H&E and Masson's trichrome. The content of hydroxyproline (HYP) and type I collagen (Col-I) were detected, while the protein expression of high-mobility group box 1 (HMGB1), transforming growth factor-beta 1 (TGF-β1), Col-I and α-smooth muscle actin (α-SMA) were analyzed by immunohistochemistry or Western blot. As observed, YTE treatment attenuated the alveolitis and fibrosis induced by BLM, reduced the loss of body weight and increase of lung coefficient. Meanwhile, YTE strongly decreased the levels of HYP and Col-I, and reduced the over-expression of HMGB1, TGF-β1, Col-I and α-SMA. In conclusion, YTE could ameliorate BLM-induced lung fibrosis by alleviating HMGB1 activity and TGF-β1 activation, suggesting therapeutic potential for PF.
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http://dx.doi.org/10.1016/j.phymed.2014.10.011DOI Listing
January 2015

Comparative genetic mapping and genomic region collinearity analysis of the powdery mildew resistance gene Pm41.

Theor Appl Genet 2014 Aug 7;127(8):1741-51. Epub 2014 Jun 7.

State Key Laboratory for Agrobiotechnology, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China.

Key Message: By applying comparative genomics analyses, a high-density genetic linkage map narrowed the powdery mildew resistance gene Pm41 originating from wild emmer in a sub-centimorgan genetic interval. Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici, results in large yield losses worldwide. A high-density genetic linkage map of the powdery mildew resistance gene Pm41, originating from wild emmer (Triticum turgidum var. dicoccoides) and previously mapped to the distal region of chromosome 3BL bin 0.63-1.00, was constructed using an F5:6 recombinant inbred line population derived from a cross of durum wheat cultivar Langdon and wild emmer accession IW2. By applying comparative genomics analyses, 19 polymorphic sequence-tagged site markers were developed and integrated into the Pm41 genetic linkage map. Ultimately, Pm41 was mapped in a 0.6 cM genetic interval flanked by markers XWGGC1505 and XWGGC1507, which correspond to 11.7, 19.2, and 24.9 kb orthologous genomic regions in Brachypodium, rice, and sorghum, respectively. The XWGGC1506 marker co-segregated with Pm41 and could be served as a starting point for chromosome landing and map-based cloning as well as marker-assisted selection of Pm41. Detailed comparative genomics analysis of the markers flanking the Pm41 locus in wheat and the putative orthologous genes in Brachypodium, rice, and sorghum suggests that the gene order is highly conserved between rice and sorghum. However, intra-chromosome inversions and re-arrangements are evident in the wheat and Brachypodium genomic regions, and gene duplications are also present in the orthologous genomic regions of Pm41 in wheat, indicating that the Brachypodium gene model can provide more useful information for wheat marker development.
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http://dx.doi.org/10.1007/s00122-014-2336-5DOI Listing
August 2014
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