scholarly journals Inferring the presence of aflatoxin-producingAspergillus flavusstrains using RNA sequencing and electronic probes as a transcriptomic screening tool

2018 ◽  
Author(s):  
Andres S. Espindola ◽  
William Schneider ◽  
Kitty F. Cardwell ◽  
Yisel Carrillo ◽  
Peter R. Hoyt ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Screening Tool ◽  
Aflatoxin Production ◽  
Specific Gene ◽  
Potato Dextrose Broth ◽  
Expression Of Genes ◽  
Bioinformatic Tool ◽  
Gene Transcripts ◽  
Nucleic Acid Analysis ◽  
Transcriptomic Level

AbstractE-probe Diagnostic for Nucleic acid Analysis (EDNA) is a bioinformatic tool originally developed to detect plant pathogens in metagenomic databases. However, enhancements made to EDNA increased its capacity to conduct hypothesis directed detection of specific gene targets present in transcriptomic databases. To target specific pathogenicity factors used by the pathogen to infect its host or other targets of interest, e-probes need to be developed for transcripts related to that function. In this study, EDNA transcriptomics (EDNAtran) was developed to detect the expression of genes related to aflatoxin production at the transcriptomic level. E-probes were designed from genes up-regulated duringA.flavusaflatoxin production. EDNAtran detected gene transcripts related to aflatoxin production in a transcriptomic database from corn, where aflatoxin was produced. The results were significantly different from e-probes being used in the transcriptomic database where aflatoxin was not produced (atoxigenic AF36 strain and toxigenic AF70 in Potato Dextrose Broth).

scholarly journals Entamoeba histolytica: Gene Expression Analysis of Cells Invading Tissues

2014 ◽  
Vol 2014 ◽  
pp. 1-5 ◽  
Author(s):  
Helen C. Fernandes ◽  
Ana F. Costa ◽  
Michelle A. R. Freitas ◽  
Almir S. Martins ◽  
Jorge L. Pesquero ◽  
...  
Keyword(s):  
Differential Expression ◽  
Entamoeba Histolytica ◽  
Virulent Strain ◽  
Protozoan Parasite ◽  
Specific Gene ◽  
Future Studies ◽  
Tissue Invasion ◽  
Expression Of Genes ◽  
Gene Transcripts ◽  
Differential Expression Of Genes

Entamoeba histolyticais a protozoan parasite that presents a risk to the health of millions of people worldwide. Due to the existence of different clinical forms caused by the parasite and also different virulence levels presented by one strain, one would expect differences in the profile of gene transcripts between virulent and nonvirulent cultures. In this study we used the differential display to select gene segments related to invasiveness of amoeba. One Brazilian strain ofE. histolyticain two conditions, able or not to cause lesions in experimental animals, was used. RNA from this strain, was used to study the differential expression of genes. 29 specific gene fragments differentially expressed in the virulent strain were selected. By real-time PCR, six of these genes had confirmed their differential expression in the virulent culture. These genes may have important roles in triggering invasive amoebiasis and may be related to adaptation of trophozoites to difficulties encountered during colonization of the intestinal epithelium and liver tissue. Future studies with these genes may elucidate its actual role in tissue invasion byE. histolyticagenerating new pathways for diagnosis and treatment of amoebiasis.

scholarly journals Global metabolic reprogramming of colorectal cancer occurs at adenoma stage and is induced by MYC

2017 ◽  
Vol 114 (37) ◽  
pp. E7697-E7706 ◽  
Author(s):  
Kiyotoshi Satoh ◽  
Shinichi Yachida ◽  
Masahiro Sugimoto ◽  
Minoru Oshima ◽  
Toshitaka Nakagawa ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cell Growth ◽  
Cancer Cells ◽  
Gene Mutations ◽  
Metabolic Reprogramming ◽  
Colorectal Carcinogenesis ◽  
Specific Gene ◽  
Control Mechanisms ◽  
Pyrimidine Synthesis ◽  
Expression Of Genes

Cancer cells alter their metabolism for the production of precursors of macromolecules. However, the control mechanisms underlying this reprogramming are poorly understood. Here we show that metabolic reprogramming of colorectal cancer is caused chiefly by aberrant MYC expression. Multiomics-based analyses of paired normal and tumor tissues from 275 patients with colorectal cancer revealed that metabolic alterations occur at the adenoma stage of carcinogenesis, in a manner not associated with specific gene mutations involved in colorectal carcinogenesis. MYC expression induced at least 215 metabolic reactions by changing the expression levels of 121 metabolic genes and 39 transporter genes. Further, MYC negatively regulated the expression of genes involved in mitochondrial biogenesis and maintenance but positively regulated genes involved in DNA and histone methylation. Knockdown of MYC in colorectal cancer cells reset the altered metabolism and suppressed cell growth. Moreover, inhibition of MYC target pyrimidine synthesis genes such as CAD, UMPS, and CTPS blocked cell growth, and thus are potential targets for colorectal cancer therapy.

scholarly journals Cold priming uncouples light- and cold-regulation of gene expression in Arabidopsis thaliana

2020 ◽  
Author(s):  
Andras Bittner ◽  
Jörn van Buer ◽  
Margarete Baier
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Plant Pathogens ◽  
Cold Treatment ◽  
Regulation Of Gene Expression ◽  
Light Regulation ◽  
High Light ◽  
Cold Stimulus ◽  
Expression Of Genes ◽  
Specific Manner

Abstract Background: The majority of stress-sensitive genes responds to cold and high light in the same direction, if plants face the stresses for the first time. As shown recently for a small selection of genes of the core environmental stress response cluster, pre-treatment of Arabidopsis thaliana with a 24 h long 4 °C cold stimulus modifies cold regulation of gene expression for up to a week at 20 °C, although the primary cold effects are reverted within the first 24 h. Such memory-based regulation is called priming. Here, we analyse the effect of 24 h cold priming on cold regulation of gene expression on a transcriptome-wide scale and investigate if and how cold priming affects light regulation of gene expression.Results: Cold-priming affected cold and excess light regulation of a small subset of genes. In contrast to the strong gene co-regulation observed upon cold and light stress in not-primed plants, most priming-sensitive genes were regulated in a stressor-specific manner in cold-primed plant. Furthermore, almost as much genes were inversely regulated as co-regulated by a 24 h long 4 °C cold treatment and exposure to heat-filtered high light (800 µmol quanta m-2 s-1). Gene ontology enrichment analysis revealed that cold priming preferentially supports expression of genes involved in the defence against plant pathogens upon cold triggering. The regulation took place on the cost of the expression of genes involved in growth regulation and transport. On the contrary, cold priming resulted in stronger expression of genes regulating metabolism and development and weaker expression of defence genes in response to high light triggering. qPCR with independently cultivated and treated replicates confirmed the trends observed in the RNASeq guide experiment.Conclusion: A 24 h long priming cold stimulus activates a several days lasting stress memory that controls cold and light regulation of gene expression and adjusts growth and defence regulation in a stressor-specific manner.

scholarly journals Specific Gene- and MicroRNA-Expression Pattern Contributes to the Epithelial to Mesenchymal Transition in a Rat Model of Experimental Colitis

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Éva Boros ◽  
Marianna Csatári ◽  
Csaba Varga ◽  
Balázs Bálint ◽  
István Nagy
Keyword(s):  
Expression Pattern ◽  
Rat Model ◽  
Epithelial To Mesenchymal Transition ◽  
Experimental Colitis ◽  
Microrna Expression ◽  
Specific Gene ◽  
Mesenchymal Transition ◽  
Expression Of Genes ◽  
Epithelial Marker ◽  
Male Wistar Rats

The aim of this study was to determine the gene- and microRNA-expression profile contributing to epithelial to mesenchymal transition in a rat model of experimental colitis. For this, inflammation was induced by injecting 2,4,6-trinitrobenzene sulphonic acid to the colon of male Wistar rats. Samples were taken from both inflamed and uninflamed regions of the same colon, total RNA was isolated, and the mRNA and microRNA expressions were monitored. We have determined that the expression of genes responsible for inducing mesenchymal phenotype, such as Egr1, Fgf2, Fgf7, Jak2, Notch2, Hif1α, Zeb2, Mmp9, Lox, and Vim, was all significantly induced in the inflamed regions of the affected colons while the epithelial marker E-cadherin (Cdh1) was downregulated. In contrast, the expression of microRNAs miR-192, miR-143, miR-375, miR-30a, miR-107, and miR-200b responsible for the regulation of the above mentioned genes was significantly downregulated in inflamed colon. Importantly, we detected moderate induction in the expression of five out of six tested microRNAs in the uninflamed regions. In summary, we identified numerous interacting genes and microRNAs with mutually exclusive expression pattern in inflamed regions of colitis-induced rats. These findings suggest that—among others—an important step in the epithelial to mesenchymal transition in experimental colitis is the dysregulated microRNA expression.

Localization and Visualization of Specific Gene Products in Fungal Plant Pathogens

2000 ◽  
Vol 6 (S2) ◽  
pp. 680-681 ◽  
Author(s):  
T. M. Bourett ◽  
K. J. Czymmek ◽  
T. M. Dezwaan ◽  
J. A. Sweigard ◽  
R. J. Howard
Keyword(s):  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Protein Localization ◽  
Infected Plant ◽  
Cell Interaction ◽  
Specific Gene ◽  
Gene Products ◽  
Tem Analysis ◽  
Fungal Plant Pathogens ◽  
Plant Pathogenesis

Specific gene products of both pathogens and hosts have been implicated as decisive elements during plant pathogenesis. While expression of some of these genes is constitutive, that of others is likely ephemeral and activated only during a particular stage of the interaction. Because the relative timing of expression may be critical, transcription and translation have often been addressed by extracting mRNA and proteins from infected plant tissue. This approach, however, cannot readily detect proteins of low abundance in bulk samples nor offer much useful information on cell-cell interaction. Only a cytological analysis that employs microscopy can resolve the temporal and spatial details of gene expression. Typically, such protein localization studies have required specific antibodies, but these large probe molecules do not diffuse into living or conventionally fixed cells of either fungal pathogens or plant hosts. For TEM analysis, these permeability-imposed limitations have been reduced by thin sectioning to render accessible antibody binding sites.

scholarly journals Epigenetics and epitranscriptomics in temporal patterning of cortical neural progenitor competence

2018 ◽  
Vol 217 (6) ◽  
pp. 1901-1914 ◽  
Author(s):  
Ki-Jun Yoon ◽  
Caroline Vissers ◽  
Guo-li Ming ◽  
Hongjun Song
Keyword(s):  
Neural Development ◽  
Molecular Mechanisms ◽  
Neural Progenitor ◽  
Developmental Competence ◽  
Mammalian Brain ◽  
Specific Gene ◽  
Lineage Specification ◽  
Regulatory Systems ◽  
Gene Transcripts ◽  
Embryonic Brain Development

During embryonic brain development, neural progenitor/stem cells (NPCs) sequentially give rise to different subtypes of neurons and glia via a highly orchestrated process. To accomplish the ordered generation of distinct progenies, NPCs go through multistep transitions of their developmental competence. The molecular mechanisms driving precise temporal coordination of these transitions remains enigmatic. Epigenetic regulation, including changes in chromatin structures, DNA methylation, and histone modifications, has been extensively investigated in the context of cortical neurogenesis. Recent studies of chemical modifications on RNA, termed epitranscriptomics, have also revealed their critical roles in neural development. In this review, we discuss advances in understanding molecular regulation of the sequential lineage specification of NPCs in the embryonic mammalian brain with a focus on epigenetic and epitranscriptomic mechanisms. In particular, the discovery of lineage-specific gene transcripts undergoing rapid turnover in NPCs suggests that NPC developmental fate competence is determined much earlier, before the final cell division, and is more tightly controlled than previously appreciated. We discuss how multiple regulatory systems work in harmony to coordinate NPC behavior and summarize recent findings in the context of a model of epigenetic and transcriptional prepatterning to explain NPC developmental competence.

scholarly journals Staphylococcus saprophyticus L-38 produces volatile 3,3-dimethyl-1,2-epoxybutane with strong inhibitory activity against Aspergillus flavus germination and aflatoxin production

2020 ◽  
Vol 13 (2) ◽  
pp. 247-258 ◽  
Author(s):  
A.D. Gong ◽  
G.J. Sun ◽  
Z.Y. Zhao ◽  
Y.C. Liao ◽  
J.B. Zhang
Keyword(s):  
Food Safety ◽  
Antifungal Activity ◽  
Aspergillus Flavus ◽  
Plant Pathogens ◽  
Aflatoxin Production ◽  
Gas Chromatography Mass Spectrometry ◽  
Total Peak Area ◽  
Staphylococcus Saprophyticus

Controlling proliferation and aflatoxin production by Aspergillus flavus is a pressing challenge for global food safety and security. Marine bacterium Staphylococcus saprophyticus strain L-38 showed excellent antifungal activity toward A. flavus in vitro and in vivo. In sealed, non-contact confrontation assays, L-38 completely inhibited conidial germination and mycelial growth of A. flavus through the production of volatile organic compounds (VOCs). Gas chromatography-mass spectrometry identified 3,3-dimethyl-1,2-epoxybutane (3-DE) as the most abundant VOC (32.61% of total peak area, 78% matching). Exposure of A. flavus cultures to synthetic 3-DE similarly demonstrated strong inhibition of growth. Moreover, culture of L-38 in a sealed chamber with maize or peanuts artificially inoculated with A. flavus, at high water activity, resulted in significant inhibition of A. flavus germination and aflatoxin biosynthesis. Scanning electron microscopy of these samples revealed severe damage to conidial cells and hyphae compared to samples not exposed to L-38. L-38 also showed broad and effective antifungal activity toward eight other phytopathogenic fungi including Aspergillus niger, Fusarium verticillioides, Fusarium graminearum, Sclerotinia sclerotiorum, Rhizoctonia solani, Alternaria alternata, Monilinia fructicola, and Botrytis cinerea. This work introduces S. saprophyticus L-38 as a potential biocontrol agent and demonstrates the efficacy of the volatile 3-DE in the control of A. flavus and other destructive plant pathogens for post-harvest food safety.

Identification of metaphase II-specific gene transcripts in porcine oocytes and their expression in early stage embryos

2005 ◽  
Vol 17 (6) ◽  
pp. 625 ◽  
Author(s):  
Xiang-Shun Cui ◽  
Hyuk Song ◽  
Nam-Hyung Kim
Keyword(s):  
Oocyte Maturation ◽  
Early Stage ◽  
Sequence Similarity ◽  
Germinal Vesicle ◽  
Specific Gene ◽  
Early Cleavage ◽  
Reverse Transcription Pcr ◽  
Gene Transcripts ◽  
Polymerase Chain ◽  
Inducible Protein

Annealing control primer (ACP)-based GeneFishing polymerase chain reaction (PCR) was used to identify the genes that are specifically or prominently expressed in porcine oocytes at the metaphase II (MII) and germinal vesicle (GV) stages. By using 60 ACPs, 13 differentially expressed genes (DEGs) were identified. The cloned genes or expressed sequence tags (ESTs) showed sequence similarity with known genes or ESTs of other species in GenBank. The mRNA expression during oocyte maturation and early embryonic development in both pigs and mice of four of these genes (namely transcription factor TZP, annexin A2, hypoxia-inducible protein 2, and ATPase 6) was further characterised by real-time quantitative reverse transcription–PCR. All four genes were markedly upregulated in pig and mouse MII oocytes compared with GV-stage oocytes. The expression levels of the four genes decreased gradually during early cleavage. Thus, these genes may play important roles during oocyte maturation and/or early cleavage in mammals. Although the detailed functions of these genes remain to be determined, their identification in the present study provides insights into meiotic maturation and fertilisation.

Prognostic impact and detection of minimal residual disease (MRD) in neuroblastoma patients.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. 10055-10055
Author(s):  
Alexander Druy ◽  
Grigory Tsaur ◽  
Alexander Popov ◽  
Tatiana Verzhbitskaya ◽  
Egor Shorikov ◽  
...  
Keyword(s):  
Roc Analysis ◽  
Residual Disease ◽  
Correct Prediction ◽  
Specific Gene ◽  
Prognostic Impact ◽  
Analytical Sensitivity ◽  
Free Survival ◽  
Genes Expression ◽  
Gene Transcripts

10055 Background: Bone marrow (BM) involvement and MRD detection in neuroblastoma (NB) seems to be useful tool for patients’ prognosis, stratification and risk-adapted treatment. Real-time PCR (RQ-PCR) of tumor-specific gene transcripts and flow cytometry (FC) are commonly applied for this purpose. Aim. RQ-PCR MRD marker definition, its qualitative concordance with FC and prognostic impact in NB patients. Methods: We analyzed 331 BM samples from 57 NB patients and 26 ‘normal’ BM samples from 20 patients without malignancies for PHOX2B, TH, ELAVL4 and GD2 genes expression. BM samples were defined as positive either in case of positivity for PHOX2B or in case of NB cells presence in BM. 326 BM samples from 52 NB patients were analyzed by RQ-PCR and FC together. Results: PHOX2B and TH were not detecting in normal BM samples. Out of 224 negative BM samples TH was identified in 5 only, while ELAVL4 and GD2 expression was detected in the majority of normal and negative BM samples: 20 and 15 from 26 normal; 209 and 197 out of 224 negative samples correspondingly. TH, ELAVL4 and GD2 expression in positive BM samples was significantly higher comparing to negative and normal BM samples.Threshold levels of each gene expression were established by ROC-analysis and subsequently applied for overall correct prediction (OCP) calculation. OCP for PHOX2B and TH achieved 0.994 and 0.952, while OCP for ELAVL4 and GD2 were significantly lower: 0.828 and 0.767 respectively. Analytical sensitivity of RQ-PCR for PHOX2B achieved 1E-06, while sensitivity of FC ranged from 1E-03 to 1E-05. In 193(59.2%) out of 326 evaluated samples BM was negative by both methods. 38(11.7%) samples were negative by FC but positive by RQ-PCR for PHOX2B expression. 31(9.5%) samples were positive by FC but negative by RQ-PCR. 64(19.6%) samples were positive by both techniques. Thus qualitative concordance between RQ-PCR and FC achieved 78.8%. Conclusions: Patients with detectable PHOX2B expression have lower event-free survival comparing to patients with PHOX2B negative BM: 0.30±0.10 and 0.77±0.27 respectively, p=0.002 and overall survival is 0.51±0.11 and 0.79±0.07 correspondingly, p=0.083. Median of follow up in our NB patients series is 42 months, ranged from 1 to 156.

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