Silencing of early auxin responsive genes MdGH3-2/12 reduces the resistance to Fusarium solani in apple

Apple replant disease(ARD)has led to severe yield and quality reduction in the apple industry.Fusarium solani(F.solani)has been identified as one of the main microbial pathogens responsible for ARD.Auxin(indole-3-acetic acid,IAA),an endogenous hormone in plants,is involved in almost all plant growth and development processes and plays a role in plant immunity against pathogens.Gretchen Hagen3(GH3)is one of the early/primary auxin response genes.The aim of this study was to evaluate the function of MdGH3-2 and MdGH3-12 in the defense response of F.solani by treating MdGH3-2/12 RNAi plants with F.solani.The results show that under F.solani infection,RNAi of MdGH3-2/12 inhibited plant biomass accumulation and exacerbated root damage.After inoculation with F.solani,MdGH3-2/12 RNAi inhibited the biosynthesis of acid-amido synthetase.This led to the inhibition of free IAA combining with amino acids,resulting in excessive free IAA accumulation.This excessive free IAA altered plant tissue structure,accelerated fungal hyphal invasion,reduced the activity of antioxidant enzymes(SOD,POD and CAT),increased the reactive oxygen species(ROS)level,and reduced total chlorophyll content and photosynthetic ability,while regulating the expression of PR-related genes including PR1,PR4,PR5 and PR8.It also changed the contents of plant hormones and amino acids,and ultimately reduced the resistance to F.solani.In conclusion,these results demonstrate that MdGH3-2 and MdGH3-12 play an important role in apple tolerance to F.solani and ARD.

Identification of ABA-responsive genes in rice shoots via cDNA macroar- ray

Phytohormone abscisic acid (ABA) was critical for many plant growth and developmental processesincluding seed maturation, germination and response to environmental factors. With the purpose to detectthe possible ABA related signal transduction pathways, we tried to isolate ABA-regulated genes throughcDNA macroarray technology using ABA-treated rice seedling as materials (under treatment for 2, 4, 8 and12 h). Of 6144 cDNA clones tested, 37 differential clones showing induction or suppression for at least onetime, were isolated. Of them 30 and 7 were up- or down-regulated respectively. Sequence analyses revealedthat the putative encoded proteins were involved in different possible processes, including transcription,metabolism and resistance, photosynthesis, signal transduction, and seed maturation. 6 cDNA clones werefound to encode proteins with unknown functions. Regulation by ABA of 7 selected clones relating to signaltransduction or metabolism was confirmed by reverse transcription PCR. In addition, some clones werefurther shown to be regulated by other plant growth regulators including auxin and brassinosteroid, which,however, indicated the complicated interactions of plant hormones. Possible signal transduction pathwaysinvolved in ABA were discussed.

Contribution of Antioxidative Enzymes and Anoxia Responsive Genes to Submergence Tolerance in Rice: A Review

Flooding/submergence of rice fields is a severe problem in South and South-East Asia, affecting more than 20 million hectares of rice every year. Submergence creates hypoxic or anoxic condition causing poor germination, seedling establishment,and enormous yield loss. Standing water in the field from weeks to months also leads to significant yield losses when large part of aerial tissues is under water. For flash flooding, a rice variety FR1A3 with tolerant gene(SUB1A) was identified. SNORKEL1 and SNORKEL2 have been identified for their ability to survive deep-water flooding by rapid elongation. Submergence stress has also been reported to adversely affect cell division and damage cellular and organelle membranes. Research on antioxidative enzymes response and genes that confer tolerance to prolonged flooding is in progress. Here we review the different anoxia responsive genes and the potential involvement of antioxidative enzymes, such as superoxide dismutase, catalase, ascorbate peroxidase and glutathione reductase, which occur in cells of rice plant exposed to submergence stress.

Identification of brassinosteroid responsive genes in Arabidopsis by cDNA array

We have systematically monitored brassinosteroid (BR) responsive genes in a BR-deficient mutant det2 suspension culture of Arabidopsis by using a cDNA array approach. Among 13000 cDNA clones arrayed on filters, 53 BR responsive clones were identified and designated BRR1-BRR53. Sequence analysis of 43 clones showed that 19 clones are novel genes, 3 clones are genes involved in the control of cell division, 4 clones are genes related to plant stress responses, 4 clones are transcriptional factor or signal transduction component genes, and 3 clones are genes involved in RNA splicing or structure forming. In addition, we also found that BR regulated the transcription of genes related to many physiological processes, such as photoreaction, ion transportation and some metabolic processes. These findings present molecular evidence that BR plays an essential role in plant growth and development.

Characterization of an Organ Specific and Pathogen Responsive CC-NBS-LRR Gene from Cotton(Gossypium hirsutum L.)

Cotton diseases represent a major challenge to cotton growth.Cloning of a cotton pathogen response gene and promoter is of great importance to improve disease resistance.In this study,a

Are Gene Expression Microarray Analyses Reliable? A Review of Studies of Retinoic Acid Responsive Genes

Microarray analyses of gene expression are widely used, but reports of the same analyses by different groups give widely divergent results, and raise questions regarding reproducibility and reliability. We take as an example recent published reports on microarray experiments that were designed to identify retinoic acid responsive genes. These reports show substantial differences in their results. In this article, we review the methodology, results, and potential causes of differences in these applications of microarrays. Finally, we suggest practices to improve the reliability and reproducibility of microarray experiments.

Bruton’s tyrosine kinase inhibitors in primary central nervous system lymphoma:New hopes on the horizon

In this editorial,we comment on the article by Wang et al.This manuscript explores the potential synergistic effects of combining zanubrutinib,a novel oral inhibitor of Bruton’s tyrosine kinase,with high-dose methotrexate(HD-MTX)as a therapeutic intervention for primary central nervous system lymphoma(PCNSL).The study involves a retrospective analysis of 19 PCNSL patients,highlighting clinicopathological characteristics,treatment outcomes,and genomic biomarkers.The results indicate the combination’s good tolerance and strong antitumor activity,with an 84.2%overall response rate.The authors emphasize the potential of zanubrutinib to modulate key genomic features of PCNSL,particularly mutations in myeloid differentiation primary response 88 and cluster of differentiation 79B.Furthermore,the study investigates the role of circulating tumor DNA in cerebrospinal fluid for disease surveillance and treatment response monitoring.In essence,the study provides valuable insights into the potential of combining zanubrutinib with HD-MTX as a frontline therapeutic regimen for PCNSL.The findings underscore the importance of exploring alternative treatment modalities and monitoring genomic and liquid biopsy markers to optimize patient outcomes.While the findings suggest promise,the study’s limitations should be considered,and further research is needed to establish the clinical relevance of this therapeutic approach for PCNSL.

Immediate-early Inducible Function in Upstream Region of junB Gene

Objective To analyze the upstream region of radiation-induced junB gene. Methods Four plasmids containing 250 bp, 590 bp, 900 bp and 1650 bp, and CAT reporter gene were constructed separately and introduced to L8704 cells. The cells were irradiated with 2 Gy X-rays and incubated at different intervals. Total RNA was extracted from the cells and fluctuation of the CAT mRNA level was assessed by the RNA ratio of CAT/β-actin measured by quantitative Northern blot hybridization. Results CAT mRNA expression containing 900 bp and 1560 bpjunB promoter remarkably and rapidly increased, and reached its peak 30min after 2 Gy X-my irradiation. Conclusions 590-900 bp fragments located in the upstream region of junB gene play an important role in the early process of cells against radiation.

Expression Changes of Early Response Genes in Lung Due to High Volume Ventilation

The expression changes of early response genes due to ventilation with high volume in adult rats in vivo were observed. Forty SD male rats were randomly divided into control and 30, 60, 90 and 120 min ventilation groups, respectively (n=8 in each group). The animals were ventilated with tidal volume of 42 ml/kg and a PEEP level of 0 cmH_2O at a rate of 40 breaths per minute in room air with a ventilator was given to the small animals. The expression of Egr-1, C-jun and IL-1β mRNA and proteins was detected by RT-PCR and immunohistochemical technique, respectively. The pathological changes in lung tissues were examined by HE staining. The results indicated that the expression of Egr-1, C-jun and IL-1β mRNA was detectable at 30th min after overventilation, but there was no significant difference in comparison with that in control group until overventilation for 60 min. However, at 90 and 120 min there was a significent increase as compared with 30 min or control group (P<0.05). The expression of Egr-1, C-jun and IL-1β deteced by immunohistochemical assay also showed a similar tendency of the gradual increase. In the 120 min ventilation group, the expression intensity of Egr-1, C-jun and IL-1β proteins in lung cells was the strongest and the nuclear translocation was increased markedly in comparison with any other groups (P<0.05). HE staining suggested that the degree of lung injury was aggravated gradually with the ventialtion going on and had a similar tendency to the expression of these early response genes and proteins. The current data suggested that overventilation activated and upregulated the expression of early response genes and the expression of these genes may be taken as the early signal to predict the onset and degree of lung injury. These results may demonstrated partially that the expression of early response genes induced by the mechanical stretch is associated with biochamic lung injury.

Evaluation of 30 DNA damage response and 6 mismatch repair gene mutations as biomarkers for immunotherapy outcomes across multiple solid tumor types

Objective:DNA damage response(DDR)genes have low mutation rates,which may restrict their clinical applications in predicting the outcomes of immune checkpoint inhibitor(ICI)treatment.Thus,a systemic analysis of multiple DDR genes is needed to identify potential biomarkers of ICI efficacy.Methods:A total of 39,631 patients with mutation data were selected from the cBioPortal database.A total of 155 patients with mutation data were obtained from the Fudan University Shanghai Cancer Center(FUSCC).A total of 1,660 patients from the MSK-IMPACT cohort who underwent ICI treatment were selected for survival analysis.A total of 249 patients who underwent ICI treatment from the Dana-Farber Cancer Institute(DFCI)cohort were obtained from a published dataset.The Cancer Genome Atlas(TCGA)level 3 RNA-Seq version 2 RSEM data for gastric cancer were downloaded from cBioPortal.Results:Six MMR and 30 DDR genes were included in this study.Six MMR and 20 DDR gene mutations were found to predict the therapeutic efficacy of ICI,and most of them predicted the therapeutic efficacy of ICI,in a manner dependent on TMB,except for 4 combined DDR gene mutations,which were associated with the therapeutic efficacy of ICI independently of the TMB.Single MMR/DDR genes showed low mutation rates;however,the mutation rate of all the MMR/DDR genes associated with the therapeutic efficacy of ICI was relatively high,reaching 10%–30%in several cancer types.Conclusions:Coanalysis of multiple MMR/DDR mutations aids in selecting patients who are potential candidates for immunotherapy.

Identification and analysis of differentially expressed genes involved in dark-induced photoperiod response and senescence of soybean leaves by suppression subtractive hybridization

A cDNA subtractive library enriched for dark-induced up-regulated ESTs was constructed by suppression subtractive hybridization(SSH) from leaf tissues of soybean cultivar DongNong L13 treated with short-day(8-h light/16-h dark) and long-day(16-h light/8-h dark) conditions.A total of 148 clones were sequenced,representing 76 unique ESTs which corresponded to about 20% of 738 clones from the cDNA library and showed a significant up-regulation of at least three fold verified by dot blot hybridization.The putative functions of ESTs were predicted by Blastn and Blastx.The 43 differentially expressed genes identified by subtractions were classified according to their putative functions generated by Blast analysis.Genetic functional analysis indicated that putative proteins encoded by these genes were related to diverse functions during organism development,which include biological regulation pathways such as transcription,signal transduction and programmed cell death,protein,nucleic acid and carbohydrate macromolecule degradation,the cell wall modification,primary and secondary metabolism and stress response.Two soybean transcription factors enhanced in SD conditions,GAMYB-binding protein and DNA binding protein RAV cDNAs that may be involved in SD soybean photoperiod response,had been isolated using 5'-and 3'-rapid amplification of cDNA ends(RACE)(Genbank Accession numbers DQ112540 and DQ147914).

Genome-wide identification, expression analysis of auxin-responsive GH_3 family genes in maize(Zea mays L.) under abiotic stresses

Auxin is involved in different aspects of plant growth and development by regulating the expression of auxin-responsive family genes. As one of the three major auxin-responsive families, GH3 (Gretchen Hagen3) genes participate in auxin homeostasis by catalyzing auxin conjugation and bounding free indole-3-acetic acid (IAA) to amino acids. However, how GH3 genes function in responses to abiotic stresses and various hormones in maize is largely unknown. Here, the latest updated maize (Zea mays L.) reference genome sequence was used to characterize and analyze the ZmGH3 family genes from maize. The results showed that 13 ZmGH3 genes were mapped on five maize chromosomes (total 10 chromosomes). Highly diversified gene structures and tissue-specific expression patterns suggested the possibility of function diversification for these genes in response to environmental stresses and hormone stimuli. The expression patterns of ZmGH3 genes are responsive to several abiotic stresses (salt, drought and cadmium) and major stress-related&nbsp;hormones (abscisic acid, salicylic acid and jasmonic acid). Various environmental factors suppress auxin free IAA contents in maize roots suggesting that these abiotic stresses and hormones might alter GH3-mediated auxin levels. The respon-siveness of ZmGH3 genes to a wide range of abiotic stresses and stress-related hormones suggested that ZmGH3s are involved in maize tolerance to environmental stresses.

Conjugated linoleic acid isomers and their precursor fatty acids regulate peroxisome proliferator-activated receptor subtypes and major peroxisome proliferator responsive element-bearing target genes in HepG2 cell model

The purpose of this study was to examine the induction profiles （as judged by quantitative reverse tran- scription polymerase chain reaction （qRT-PCR）） of peroxisome proliferator-activated receptor （PPAR） α,β, y subtypes and major PPAR-target genes bearing a functional peroxisome proliferator responsive element （PPRE） in HepG2 cell model upon feeding with cis-9,trans-11-octadecadienoic acid （9-CLA） or trans-10,cis-12-octadecadienoic acid （10-CLA） or their precursor fatty acids （FAs）. HepG2 cells were treated with 100 pmol/L 9-CLA or 10-CLA or their precursor FAs, viz., oleic, linoleic, and trans-11-vaccenic acids against bezafibrate control to evaluate the induc- tion/expression profiles of PPAR （α, β, γ subtypes and major PPAR-target genes bearing a functional PPRE, i.e., fatty acid transporter （FAT）, glucose transporter-2 （GLUT-2）, liver-type FA binding protein （L-FABP）, acyl CoA oxidase-1 （ACOX-1）, and peroxisomal bifunctional enzyme （PBE） with reference to β-actin as house keeping gene. Of the three housekeeping genes （glyceraldehyde 3-phosphate dehydrogenase （GAPDH）, β-actin, and ubiquitin）, β-actin was found to be stable. Dimethyl sulfoxide （DMSO）, the common solubilizer of agonists, showed a significantly higher induction of genes analyzed, qRT-PCR profiles of CLAs and their precursor FAs clearly showed upregulation of FAT, GLUT-2, and L-FABP （-0.5-.0-fold）. Compared to 10-CLA, 9-CLA decreased the induction of the FA metabolizing gene ACOX-1 less than did PBE, while 10-CLA decreased the induction of PBE less than did ACOX-I. Both CLAs and precursor FAs upregulated PPRE-beadng genes, but with comparatively less or marginal activation of PPAR subtypes This indicates that the binding of CLAs and their precursor FAs to PPAR subtypes results in PPAR activation, thereby induction of the target transporter genes coupled with downstream lipid metabolising genes such as ACOX-1 and PBE. To sum up, the expression profiles of these candidate genes showed that CLAs and their precursor FAs are involved in lipid signalling by modulating the PPAR a, 13, or ~ subtype for the indirect activation of the PPAR-target genes, which may in turn be responsible for the supposed health effects of CLA, and that care should be taken while calculating the actual fold induction values of candidate genes with reference to housekeeping gene and DMSO as they may impart false positive results.

Eukaryotic expression of outer membrane protein Gpd from Treponema pallidum and preliminary studies on its immune response in rabbits

The Gpd gene was amplified from the genomic DNA of Treponema the appropriate site of pcDNA3.1 （ ＋ ） vector. The expression of pcDNA3. I was tested with Western blotting and technology of immunoeytochemisty. New munized with the eukaryotic expression recombinant pcDNA3, 1 （ ＋ ）-Gpd pallidum and cloned into （ ＋ ）-Gpd in Hel,a cells Zealand rabbits were imA fusion protein of C, pd with 4.1 kDa has been effectively expressed in HeLa cells, which were detected bv Western blotting and the immunocytochemistry techniques. The New Zealand rabbits were able to elicit the specific antibody after immunization with the nucleic acid vaccine. The antibody titer could reach as high as 1 ： 1024 after 2 weeks of the third injection; and the splenocytes proliferated evidently due to the Gpd protein stimulation. Both the antibody titer and the splenocytes proliferation were higher substantially than those of controls （ P 〈 0.01 ）. All above data will contribute to an experimental basis of further study of the biological function of Gpd protein as well as DNA vaccine for syphilis.

Drosophila Ortholog of Mammalian Immediate-Early Gene Npas4 is Specifically Responsive to Reversal Learning

Dear Editor,In dynamic environments,the memory system of the brain must be able to perceive and process conflicting experiences to reach an adaptive decision.In Drosophila,in contrast to consistent experiences,conflicting experiences trigger significantly increased Rac1 activity which mediates active forgetting [1].The ability to cope with conflicting experiences but not simple learning experiences is impaired in mutants of multiple autism-risk genes [2].

Ethylene Response Factor TERF1 Enhances Glucose Sensitivity in Tobacco through Activating the Expression of Sugar-related Genes

Ethylene response factor （ERF） proteins are important plant-specific transcription factors. Increasing evidence shows that ERF proteins regulate plant pathogen resistance, abiotic stress response and plant development through interaction with different stress responsive pathways. Previously, we revealed that overexpression of TERF1 in tobacco activates a cluster gene expression through interacting with GCC box and dehydration responsive element （DRE）, resulting in enhanced sensitivity to abscisic acid （ABA） and tolerance to drought, and dark green leaves of mature plants, indicating that TERF1 participates in the integration of ethylene and osmotic responses. Here we further report that overexpression of TERF1 confers sugar response in tobacco. Analysis of the novel isolated tomato TERF1 promoter provides information indicating that there are many cis-acting elements, including sugar responsive elements （SURE） and W box, suggesting that TERF1 might be sugar inducible. This prediction is confirmed by results of reverse transcription-polymerase chain reaction amplification, indicating that transcripts of TERF1 are accumulated in tomato seedlings after application of glucose. Further investigation indicates that the expression of TERF1 in tobacco enhances sensitivity to glucose during seed germination, root and seedling development, showing a decrease of the fresh weight and root elongation under glucose treatment. Detailed investigations provide evidence that TERF1 interacts with the sugar responsive cis-acting element SURE and activates the expression of sugar response genes, establishing the transcriptional regulation of TERF1 in sugar response. Therefore, our results deepen our understanding of the glucose response mediated by the ERF protein TERF1 in tobacco.

Response gene to complement 32 （RGC-32） expression on M2-polarized and tumor-associated macrophages is M-CSF-dependent and enhanced by tumor-derived IL-4

Response gene to complement 32 （RGC-32） is a cell cycle regulator involved in the proliferation, differentiation and migration of cells and has also been implicated in angiogenesis. Here we show that RGC-32 expression in macrophages is induced by IL-4 and reduced by LPS, indicating a link between RGC-32 expression and M2 polarization. We demonstrated that the increased expression of RGC-32 is characteristic of alternatively activated macrophages, in which this protein suppresses the production of pro-inflammatory cytokine IL-6 and promotes the production of the anti-inflammatory mediator TGF-β. Consistent with in vitro data, tumor-associated macrophages （TAMs） express high levels of RGC-32, and this expression is induced by tumor-derived ascitic fluid in an M-CSF- and/or IL-4-dependent manner. Collectively, these results establish RGC-32 as a marker for M2 macrophage polarization and indicate that this protein is a potential target for cancer immunotherapy, targeting tumor-associated macrophages.

Gene mutation in patients with primary open angle glaucoma in a pedigree in China

Objective To investigate the genetic basis of the pathogenesis of a Guangzhou (GZ 1) pedigree with primary open angle glaucoma (POAG) Methods DNA fragments of the trabecular meshwork inducible glucocorticoid response protein (TIGR) gene from 4 typical POAG patients and 2 normal subjects were amplified by polymerase chain reaction (PCR) The amplified PCR fragment was cloned into a pT Adv vector, and direct sequencing was carried out on an ABI 373 automated DNA sequencer using dye terminator chemistry to detect the mutation Results The TIGR gene mutation was identified in the selected subjects of this pedigree This mutation is a “C to T” transition at position 370, different from that of western countries and equivalent to the position change found in Japanese patients with familial POAG No mutation was found in the TIGR gene fragment in 2 normal subjects of the pedigree Conclusions These preliminary results provide insights into the pathogenesis of POAG by the TIGR gene mutation, and into the underlying action of the different mutations in oriental and western peoples

Genome-wide identification and characterization of phospholipase C gene family in cotton (Gossypium spp.)

Phospholipase C (PLC) are important regulatory enzymes involved in several lipid and Ca2+-dependent signaling pathways.Previous studies have elucidated the versatile roles of PLC genes in growth, development and stress responses of many plants, however, the systematic analyses of PLC genes in the important fiber-producing plant, cotton, are still deficient. In this study,through genome-wide survey, we identified twelve phosphatidylinositol-specific PLC (PI-PLC) and nine non-specific PLC (NPC) genes in the allotetraploid upland cotton Gossypium hirsutum and nine PI-PLC and six NPC genes in two diploid cotton G. arboretum and G.raimondii, respectively. The PI-PLC and NPC genes of G. hirsutum showed close phylogenetic relationship with their homologous genes in the diploid cottons and Arabidopsis. Segmental and tandem duplication contributed greatly to the formation of the gene family. Expression profiling indicated that few of the PLC genes are constitutely expressed, whereas most of the PLC genes are preferentially expressed in specific tissues and abiotic stress conditions. Promoter analyses further implied that the expression of these PLC genes might be regulated by MYB transcription factors and different phytohormones.These results not only suggest an important role of phospholipase C members in cotton plant development and abiotic stress response but also provide good candidate targets for future molecular breeding of superior cotton cultivars.

Mapping of Defense Response Gene Homologs and Their Association with Resistance Loci in Maize

Defense response genes in higher plant species are involved in a variety of signal transduction pathways and biochemical reactions to counterattack invading pathogens. In this study, a total of 366 non-redundant defense response gene homologs （DRHs）, including 124 unigenes/expressed sequence tags, 226 tentative consensuses, and 16 DRH contigs have been identified by mining the Maize Genetics and Genomics and The Institute for Genomic Research maize databases using 35 essential defense response genes. Of 366 DRHs, 202 are mapped to 152 loci across ten maize chromosomes via both the genetic and in silico mapping approaches. The mapped DRHs seem to cluster together rather than be evenly distributed along the maize genome. Approximately half of these DHRs are located in regions harboring either major resistance genes or quantitative trait loci （QTL）. Therefore, this comprehensive DRH linkage map will provide reference sequences to identify either positional candidate genes for resistance genes and/or QTLs or to develop makers for fine-mapping and marker-assisted selection of resistance genes and/or QTLs.