Transcription factors leading the pathway to survival

Abstract only availableAsian Soybean Rust, a foliar disease, is caused by the fungal pathogen Phakospora pachyrhizi, which threatens soybean (Glycine max) production in many countries. In the absence of fungicide treatment, yield losses from ASR can be up to 80%. The use of fungicides significantly drives up production costs for farmers. Four resistant genes, Rpp1-4, have been identified for ASR but none of these provide sustained, field resistance due to adaptation by the pathogen. Soybean cultivar Williams 82 is susceptible to ASR, while cultivar DT2000 exhibits significant levels of tolerance to the pathogen. We utilized these two cultivars to examine the differential response in the expression of various transcription factor genes to ASR inoculation. Our goal is to identify transcription factors that contribute to soybean resistance to ASR and to identify the corresponding genes and pathways responsible for resistance. Due to the -relatively low abundance of TF gene mRNA, we utilized the qRT-PCR technique to accurately assay gene expression. We also examined the progress of ASR infection by staining infected leaves at different time points after inoculation. In this way, we hope to correlate the expression of specific genes with the stage of infection. After some trial and error, we were able to easily visualize ASR infection in soybean leaves by staining with Calcofluor White. This staining method allowed us to track ASR infection and document the various stages of fungal development. Our initial screens for TF gene expression identified a few TF genes that are clearly differentially expressed between the susceptible and resistance soybean cultivars. We hope in further experiments to understand the function of these TF genes in soybean resistance to ASR and, ultimately, contribute to the development of soybean cultivars that will benefit soybean farmers.NSF grant to G. Stace

Generation of Phaseolus vulgaris ESTs and investigation of their regulation upon Uromyces appendiculatus infection

<p>Abstract</p> <p>Background</p> <p><it>Phaseolus vulgaris </it>(common bean) is the second most important legume crop in the world after soybean. Consequently, yield losses due to fungal infection, like <it>Uromyces appendiculatus </it>(bean rust), have strong consequences. Several resistant genes were identified that confer resistance to bean rust infection. However, the downstream genes and mechanisms involved in bean resistance to infection are poorly characterized.</p> <p>Results</p> <p>A subtractive bean cDNA library composed of 10,581 unisequences was constructed and enriched in sequences regulated by either bean rust race 41, a virulent strain, or race 49, an avirulent strain on cultivar Early Gallatin carrying the resistance gene <it>Ur-4</it>. The construction of this library allowed the identification of 6,202 new bean ESTs, significantly adding to the available sequences for this plant. Regulation of selected bean genes in response to bean rust infection was confirmed by qRT-PCR. Plant gene expression was similar for both race 41 and 49 during the first 48 hours of the infection process but varied significantly at the later time points (72–96 hours after inoculation) mainly due to the presence of the <it>Avr4 </it>gene in the race 49 leading to a hypersensitive response in the bean plants. A biphasic pattern of gene expression was observed for several genes regulated in response to fungal infection.</p> <p>Conclusion</p> <p>The enrichment of the public database with over 6,000 bean ESTs significantly adds to the genomic resources available for this important crop plant. The analysis of these genes in response to bean rust infection provides a foundation for further studies of the mechanism of fungal disease resistance. The expression pattern of 90 bean genes upon rust infection shares several features with other legumes infected by biotrophic fungi. This finding suggests that the <it>P. vulgaris</it>-<it>U. appendiculatus </it>pathosystem could serve as a model to explore legume-rust interaction.</p

A TMEFF2-regulated cell cycle derived gene signature is prognostic of recurrence risk in prostate cancer

Background: The clinical behavior of prostate cancer (PCa) is variable, and while the majority of cases remain indolent, 10% of patients progress to deadly forms of the disease. Current clinical predictors used at the time of diagnosis have limitations to accurately establish progression risk. Here we describe the development of a tumor suppressor regulated, cell-cycle gene expression based prognostic signature for PCa, and validate its independent contribution to risk stratification in several radical prostatectomy (RP) patient cohorts. Methods: We used RNA interference experiments in PCa cell lines to identify a gene expression based gene signature associated with Tmeff2, an androgen regulated, tumor suppressor gene whose expression shows remarkable heterogeneity in PCa. Gene expression was confirmed by qRT-PCR. Correlation of the signature with disease outcome (time to recurrence) was retrospectively evaluated in four geographically different cohorts of patients that underwent RP (834 samples), using multivariate logistical regression analysis. Multivariate analyses were adjusted for standard clinicopathological variables. Performance of the signature was compared to previously described gene expression based signatures using the SigCheck software. Results: Low levels of TMEFF2 mRNA significantly (p \u3c 0.0001) correlated with reduced disease-free survival (DFS) in patients from the Memorial Sloan Kettering Cancer Center (MSKCC) dataset. We identified a panel of 11 TMEFF2 regulated cell cycle related genes (TMCC11), with strong prognostic value. TMCC11 expression was significantly associated with time to recurrence after prostatectomy in four geographically different patient cohorts (2.9 ≤ HR ≥ 4.1; p ≤ 0.002), served as an independent indicator of poor prognosis in the four RP cohorts (1.96 ≤ HR ≥ 4.28; p ≤ 0.032) and improved the prognostic value of standard clinicopathological markers. The prognostic ability of TMCC11 panel exceeded previously published oncogenic gene signatures (p = 0.00017). Conclusions: This study provides evidence that the TMCC11 gene signature is a robust independent prognostic marker for PCa, reveals the value of using highly heterogeneously expressed genes, like Tmeff2, as guides to discover prognostic indicators, and suggests the possibility that low Tmeff2 expression marks a distinct subclass of PCa

Enhancing Our Understanding of Plant Cell-to-Cell Interactions Using Single-Cell Omics

Plants are composed of cells that physically interact and constantly adapt to their environment. To reveal the contribution of each plant cells to the biology of the entire organism, their molecular, morphological, and physiological attributes must be quantified and analyzed in the context of the morphology of the plant organs. The emergence of single-cell/nucleus omics technologies now allows plant biologists to access different modalities of individual cells including their epigenome and transcriptome to reveal the unique molecular properties of each cell composing the plant and their dynamic regulation during cell differentiation and in response to their environment. In this manuscript, we provide a perspective regarding the challenges and strategies to collect plant single-cell biological datasets and their analysis in the context of cellular interactions. As an example, we provide an analysis of the transcriptional regulation of the Arabidopsis genes controlling the differentiation of the root hair cells at the single-cell level. We also discuss the perspective of the use of spatial profiling to complement existing plant single-cell omics

Involvement of the xyloglucan endotransglycosylase/hydrolases encoded by celery XTH1 and Arabidopsis XTH33 in the phloem response to aphids

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Transcriptome analysis of the phloem of in the plant response to aphid feeding

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Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume

International audienceMedicago truncatula is a model legume species that has been studied for decades to understand the symbiotic relationship between legumes and soil bacteria collectively named rhizobia. This symbiosis called nodulation is initiated in roots with the infection of root hair cells by the bacteria as well as the initiation of nodule primordia from root cortical, endodermal, and pericycle cells, leading to the development of a new root organ, the nodule, where bacteria fix and assimilate the atmospheric dinitrogen for the benefit of the plant. Here, we report the isolation and use of nuclei from mock and rhizobia-inoculated roots to conduct single nuclei RNA-seq (sNucRNA-seq) experiments to gain a deeper understanding of early responses to rhizobial infection in Medicago roots. A gene expression map of the Medicago root was generated, comprising 25 clusters, which were annotated as specific cell-types using 119 Medicago marker genes and orthologs to Arabidopsis cell-type marker genes. A focus on root hair, cortex, endodermis, and pericycle cell-types, showing the strongest differential regulations in response to a short-term (48 hours) rhizobium inoculation, revealed both known genes and functional pathways, validating the sNucRNA-seq approach, but also numerous novel genes and pathways, allowing a comprehensive analysis of early root symbiotic responses at a cell-type-specific level

Systemic response to aphid infestation by Myzus persicae in the phloem of apuim graveolens

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