The Application of Genomic Approaches in Studying a Bacterial Blight-Resistant Mutant in Rice

Rice bacterial blight disease (BBD), caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the serious diseases in most rice production regions. In this report, we screened for resistance mutants from the mutation pool of TNG67 variety derived by sodium azide (SA) mutagenesis with phenotype investigation and assisted with fluorescent detection. SA0423 is a mutant of broad range resistance against Xoo for many years; the resistance was studied following the concept of central dogma. The inheritance of resistance was characterized, and three QTLs were mapped onto the genome of SA0423 using simple sequence repeat (SSR) markers and R/qtl by genomic approach. In transcriptomic approach, only one differential expression QTLs (eQTLs) were identified; two differentially expressed proteins (pQTLs) were identified and genetically characterized by proteomics after Xoo challenged in SA0423 mutant. To improve the bacterial blight resistance, makers are developed from QTLs, eQTLs and pQTLs to pyramid the resistance genes through marker-assisted breeding in our rice breeding programs

A unique distant submillimeter galaxy with an X-ray-obscured radio-luminous active galactic nucleus

We present a multiwavelength study of an atypical submillimeter galaxy in the GOODS-North field, with the aim to understand its physical properties of stellar and dust emission, as well as the central AGN activity. Although it is shown that the source is likely an extremely dusty galaxy at high redshift, its exact position of submillimeter emission is unknown. With the new NOEMA interferometric imaging, we confirm that the source is a unique dusty galaxy. It has no obvious counterpart in the optical and even NIR images observed with HST at lambda~<1.4um. Photometric-redshift analyses from both stellar and dust SED suggest it to likely be at z~>4, though a lower redshift at z~>3.1 cannot be fully ruled out (at 90% confidence interval). Explaining its unusual optical-to-NIR properties requires an old stellar population (~0.67 Gyr), coexisting with a very dusty ongoing starburst component. The latter is contributing to the FIR emission, with its rest-frame UV and optical light being largely obscured along our line of sight. If the observed fluxes at the rest-frame optical/NIR wavelengths were mainly contributed by old stars, a total stellar mass of ~3.5x10^11Msun would be obtained. An X-ray spectral analysis suggests that this galaxy harbors a heavily obscured AGN with N_H=3.3x10^23 cm^-2 and an intrinsic 2-10 keV luminosity of L_X~2.6x10^44 erg/s, which places this object among distant type 2 quasars. The radio emission of the source is extremely bright, which is an order of magnitude higher than the star-formation-powered emission, making it one of the most distant radio-luminous dusty galaxies. The combined characteristics of the galaxy suggest that the source appears to have been caught in a rare but critical transition stage in the evolution of submillimeter galaxies, where we are witnessing the birth of a young AGN and possibly the earliest stage of its jet formation and feedback.Comment: 13 pages in printer format, 10 figures, 1 table, accepted for publication in the A&

Ke Hsin Kuo: A distinguished scientist and great mentor

This paper is dedicated to the 95th birthday anniversary of Professor Ke Hsin Kuo. Professor Ke Hsin Kuo (郭可信, Guo Kexin, 1923–2006) was a pioneer in the development of electron microscopy for materials research. He also played a key role in introducing cryo-electron microscopy for structural biology research in China. He was an Academician of the Chinese Academy of Sciences, a Foreign Member of the Royal Swedish Academy of Engineering, a former President of the Chinese Electron Microscopy Society, and a winner of the First Class National Science Medal of China. He trained close to 130 graduate students over 50 years. His contributions to high-resolution electron microscopy, especially in the studies of quasicrystals, as well as his achievements in training and promoting younger scientists, had a profound impact on the field that continues to benefit and inspire many who had the fortune to be his pupil, to have worked with him, or to have followed his footsteps

1-Metilciklopropen ublažava oštećenja mahuna tijekom skladištenja pri niskim temperaturama povećanjem učinka antioksidacijskog sustava stanične zaštite

Research background. Chilling injury is a major disorder affecting the quality of tropical and subtropical vegetables during low temperature storage. Snap bean (Phaseolus vulgaris L.) is sensitive to chilling injury. The main purpose of the present study is to investigate the alleviating effects of 1-methylcyclopropene (1-MCP) on chilling injury of snap bean. In addition, the related mechanisms were also detected from the perspective of the changes of antioxidant defense system. Experimental approach. Snap beans were exposed to different volume fractions of 1-MCP. After 24 h of treatment, snap beans were stored at 4 °C for up to 14 days. Chilling injury index, electrolyte leakage, titratable acidity and total soluble solids were determined. Contents of chlorophyll, ascorbic acid and malondialdehyde were assessed. The total antioxidant capacity, Fe(II) ion chelating capacity, scavenging capacities on free radicals and activities of antioxidant enzymes were detected. Total phenol content and activities of related metabolic enzymes were also determined. Results and conclusions. 1-MCP treatment reduced chilling injury index, electrolyte leakage rate and malondialdehyde content of snap beans. The amounts of total soluble solids, titratable acid, ascorbic acid and total chlorophyll in 1-MCP-treated snap beans were significantly higher than those of control. The snap beans treated with 1-MCP showed stronger total antioxidant capacity and metal chelating activity. The 1-MCP treatment enhanced scavenging effects of snap beans on superoxide, hydroxyl and 1,1-diphenyl-2-trinitrophenylhydrazine radicals. The activities of peroxidase, ascorbate peroxidase, superoxide dismutase and catalase in 1-MCP-treated group were higher than of control. The treatment also enhanced the accumulation of phenolic compounds in snap beans by regulating the activities of phenol-metabolizing enzymes such as shikimate dehydrogenase, phenylalanine ammonia lyase enzyme, cinnamic acid 4-hydroxylase and polyphenol oxidase. In conclusion, with the mechanism that involves the activation of enzymatic and non-enzymatic antioxidant systems, 1-MCP has the ability to avoid chilling injury of snap bean. Novelty and scientific contribution. This study gives insights into whether 1-MCP can regulate postharvest cold resistance in vegetables by enhancing the enzymatic antioxidant system and inducing the accumulation of non-enzymatic antioxidants. Considering the results, 1-MCP treatment could be an effective method to alleviate postharvest chilling injury of snap beans during low temperature storage.Pozadina istraživanja. Oštećenje ploda tijekom skladištenja pri niskim temperaturama jedan je od primarnih uzroka smanjenja kakvoće tropskog i suptropskog povrća. Grah (Phaseolus vulgaris L.) je osjetljiv na oštećenja pri niskim temperaturama. Stoga je glavna svrha ovoga rada bila ispitati ublažavajući učinak 1-metilciklopropena na oštećenja mahuna pri niskim temperaturama. Osim toga, utvrđeni su mehanizmi promjene obrambenog antioksidacijskog sustava. Eksperimentalni pristup. Mahune su izložene različitim volumnim udjelima 1-metilciklopropena tijekom 24 sata. Nakon toga su uzorci mahuna skladišteni pri 4 °C do 14 dana. Mjereni su sljedeći parametri: indeks oštećenja pri niskim temperaturama, gubitak elektrolita, titracijska kiselost i udjel ukupnih topljivih tvari. Osim toga, utvrđeni su udjeli klorofila, askorbinske kiseline i malondialdehida. Određeni su ukupni antioksidacijski učinak, sposobnost keliranja Fe(II) iona, sposobnost uklanjanja reaktivnih kisikovih spojeva i aktivnost antioksidacijskih enzima. Također su određeni ukupni udjel fenola i s njima povezana metabolička aktivnost enzima. Rezultati i zaključci. Nakon obrade 1-metilciklopropenom smanjili su se indeks oštećenja pri niskim temperaturama, gubitak elektrolita i udjel malondialdehida u mahunama. Količine ukupnih topljivih suhih tvari, titracijske kiselosti, askorbinske kiseline i ukupnog klorofila u mahunama izloženim 1-metilciklopropenu bile su znatno veće nego u kontrolnom uzorku. Tretirane mahune imale su veću ukupnu antioksidacijsku aktivnost i sposobnost keliranja metala. Obradom 1-metilciklopropenom povećala se sposobnost uklanjanja radikala superoksida, hidroksila i 1,1-difenil-2-trinitrofenilhidrazina u mahunama. Aktivnosti peroksidaze, askorbat peroksidaze, superoksid dismutaze i katalaze bile su veće u tretiranim nego u kontrolnim uzorcima. Osim toga, obradom se povećalo nakupljanje fenolnih spojeva zbog regulacije enzima koji sudjeluju u metabolizmu fenola, kao što su šikimat-dehidrogenaza, fenilalanin amonijak-liaza, p-kumarinska kiselina i polifenol-oksidaza. Možemo zaključiti da 1-metilciklopropen može spriječiti oštećenje mahuna pri niskim temperaturama aktivacijom enzimskih i neenzimskih antioksidacijskih sustava. Novina i znanstveni doprinos. Ovaj rad daje uvid u mogućnost regulacije otpornosti povrća na niske temperature tijekom skladištenja poboljšanjem enzimskog antioksidacijskog sustava pomoću 1-metilciklopropena te nakupljanjem neenzimskih antioksidanasa. Dobiveni rezultati pokazuju da bi obrada 1-metilciklopropenom mogla biti učinkovita metoda ublažavanja oštećenja pri niskim temperaturama tijekom skladištenja graha

GPR48-Induced keratinocyte proliferation occurs through HB-EGF mediated EGFR transactivation

AbstractGPR48 can mediate keratinocyte proliferation and migration. Our investigations showed that AG1478, an inhibitor of EGFR tyrosine kinase, could block GPR48-mediated cellular processes. AG1478 treatment of Gpr48+/+ cells also decreased phosphorylation of EGFR, ERK and STAT3. Subsequent screening using conditioned media immunodepleted of EGFR ligands identified HB-EGF as the ligand responsible for phosphorylation of EGFR, ERK and STAT3. HB-EGF was reduced in Gpr48−/− cell culture medium, but its addition restored the phosphorylation of EGFR, ERK, STAT3, as well as cell proliferation. Confirmation that GPR48 mediates EGFR signaling pathway through HB-EGF was subsequently performed using an inhibitor of HB-EGF

miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs), small non-coding RNAs of 19 to 25 nt, play important roles in gene regulation in both animals and plants. In the last few years, the oligonucleotide microarray is one high-throughput and robust method for detecting miRNA expression. However, the approach is restricted to detecting the expression of known miRNAs. Second-generation sequencing is an inexpensive and high-throughput sequencing method. This new method is a promising tool with high sensitivity and specificity and can be used to measure the abundance of small-RNA sequences in a sample. Hence, the expression profiling of miRNAs can involve use of sequencing rather than an oligonucleotide array. Additionally, this method can be adopted to discover novel miRNAs.</p> <p>Results</p> <p>This work presents a systematic approach, miRExpress, for extracting miRNA expression profiles from sequencing reads obtained by second-generation sequencing technology. A stand-alone software package is implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes. The software is also a database-supported, efficient and flexible tool for investigating miRNA regulation. Moreover, we demonstrate the utility of miRExpress in extracting miRNA expression profiles from two Illumina data sets constructed for the human and a plant species.</p> <p>Conclusion</p> <p>We develop miRExpress, which is a database-supported, efficient and flexible tool for detecting miRNA expression profile. The analysis of two Illumina data sets constructed from human and plant demonstrate the effectiveness of miRExpress to obtain miRNA expression profiles and show the usability in finding novel miRNAs.</p