scholarly journals The effects of the neonicotinoid imidacloprid on gene expression and DNA methylation in the buff-tailed bumblebee Bombus terrestris

2019 ◽  
Author(s):  
P.S.A Bebane ◽  
B.J. Hunt ◽  
M. Pegoraro ◽  
A.R.C Jones ◽  
H. Marshall ◽  
...  
Keyword(s):  
Sublethal Effects ◽  
Bombus Terrestris ◽  
Low Doses ◽  
Large Array ◽  
Epigenetic Changes ◽  
Rna Seq ◽  
Nicotinic Acetylcholine ◽  
Horticultural Crops ◽  
Highly Expressed Genes ◽  
And Control

AbstractNeonicotinoids are effective insecticides used on many important arable and horticultural crops. They are nicotinic acetylcholine receptor agonists which disrupt the function of insect neurons and cause paralysis and death. In addition to direct mortality, there are numerous sublethal effects of low doses of neonicotinoids on bees. We hypothesize that some of these large array of effects could be a consequence of epigenetic changes in bees induced by neonicotinoids. We compared whole methylome (BS-seq) and RNA-seq libraries of the brains of buff tailed bumblebee Bombus terrestris workers exposed to field realistic doses of the neonicotinoid imidacloprid to libraries from control workers. We found numerous genes which show differential expression between neonicotinoid treated bees and control bees, but no differentially methylated cytosines in any context. We found CpG methylation to be focused mainly in exons and associated with highly expressed genes. We discuss the implications of our results for future legislation.

scholarly journals The effects of the neonicotinoid imidacloprid on gene expression and DNA methylation in the buff-tailed bumblebee Bombus terrestris

2019 ◽  
Vol 286 (1905) ◽  
pp. 20190718 ◽  
Author(s):  
P. S. A. Bebane ◽  
B. J. Hunt ◽  
M. Pegoraro ◽  
A. R. C Jones ◽  
H. Marshall ◽  
...  
Keyword(s):  
Sublethal Effects ◽  
Bombus Terrestris ◽  
Low Doses ◽  
Large Array ◽  
Epigenetic Changes ◽  
Rna Seq ◽  
Nicotinic Acetylcholine ◽  
Horticultural Crops ◽  
Highly Expressed Genes ◽  
And Control

Neonicotinoids are effective insecticides used on many important arable and horticultural crops. They are nicotinic acetylcholine receptor agonists which disrupt the function of insect neurons and cause paralysis and death. In addition to direct mortality, there are numerous sublethal effects of low doses of neonicotinoids on bees. We hypothesize that some of these large array of effects could be a consequence of epigenetic changes in bees induced by neonicotinoids. We compared whole methylome (BS-seq) and RNA-seq libraries of the brains of buff-tailed bumblebee Bombus terrestris workers exposed to field-realistic doses of the neonicotinoid imidacloprid to libraries from control workers. We found numerous genes which show differential expression between neonicotinoid-treated bees and control bees, but no differentially methylated cytosines in any context. We found CpG methylation to be focused mainly in exons and associated with highly expressed genes. We discuss the implications of our results for future legislation.

Comparative expression profiling of three early inflorescence stages of oil palm indicates that vegetative to reproductive phase transition of meristem is regulated by sugar balance

2015 ◽  
Vol 42 (6) ◽  
pp. 589 ◽  
Author(s):  
Walter Ajambang ◽  
Sintho W. Ardie ◽  
Hugo Volkaert ◽  
Georges F. Ngando-Ebongue ◽  
Sudarsono Sudarsono
Keyword(s):  
Oil Palm ◽  
Rna Seq ◽  
Illumina Platform ◽  
Reproductive Phase ◽  
Underlying Network ◽  
Highly Expressed Genes ◽  
Three Stages ◽  
Stage 1 ◽  
And Control ◽  
Gene Expression Levels

Breeding and seed production activities in oil palm have been hampered because of the inability of the male parent Pisifera to produce male inflorescence as source of pollen under normal conditions. Researchers are using complete defoliation to induce male inflorescences, but the biological and molecular processes responsible for this morphological change are yet to be revealed. To understand the underlying network of genes that initiate and control this phenotypically documented activity, we initiated a study aimed at identifying differentially expressed genes (DEGs) in three stages of an oil palm inflorescence under complete defoliation stress using RNA-seq. Sequencing on an Illumina platform produced 82 631 476 reads consisting of 8 345 779 076 bases. A total of 60 700 genes were obtained after transcript filtering and normalisation and 54% of them were downregulated. Differences in gene expression levels were significant between tissues under stress. The farther the distance between tissues, the more DEGs recorded. Comparison between stage 2 and stage 1 induced 3893 DEGs whereas 10 136 DEGs were induced between stage 3 and stage 1. Stress response genes and flower development genes were among the highly expressed genes. This study suggests a link between complete defoliation and meristem differentiation from vegetative to reproductive phase in oil palm.

Suppressed Immune-Related Profile Rescues Abortion-Prone Fetuses: A Novel Insight Into the CBA/J × DBA/2J Mouse Model

2019 ◽  
Vol 26 (11) ◽  
pp. 1485-1492
Author(s):  
Xiaochun Yi ◽  
Jie Zhang ◽  
Huixiang Liu ◽  
Tianxia Yi ◽  
Yuhua Ou ◽  
...  
Keyword(s):  
Immune System ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Poor Treatment ◽  
Polymerase Chain ◽  
Poor Treatment Outcome ◽  
Immune Related Genes ◽  
And Control ◽  
Upregulated Genes ◽  
Tgf Β1

The adverse clinical result and poor treatment outcome in recurrent spontaneous abortion (RSA) make it necessary to understand the pathogenic mechanism. The mating combination CBA/J × DBA/2 has been widely used as an abortion-prone model compared to DBA/2-mated CBA/J mice. Here, we used RNA-seq to get a comprehensive catalogue of genes differentially expressed between survival placenta in abortion-prone model and control. Five hundred twenty-four differentially expressed genes were obtained followed by clustering analysis, Gene Ontology analysis, and pathway analysis. We paid more attention to immune-related genes namely “immune response” and “immune system process” including 33 downregulated genes and 28 upregulated genes. Twenty-one genes contribute to suppressing immune system and 7 are against it. Six genes were validated by reverse transcription-polymerase chain reaction, namely Ccr1l1, Tlr4, Tgf-β1, Tyro3, Gzmb, and Il-1β. Furthermore, Tlr4, Tgf-β1, and Il-1β were analyzed by Western blot. Such immune profile gives us a better understanding of the complicated immune processing in RSA and immunosuppression can rescue pregnancy loss.

scholarly journals Dual Role of Integrin Alpha-6 in Glioblastoma: Supporting Stemness in Proneural Stem-Like Cells While Inducing Radioresistance in Mesenchymal Stem-Like Cells

Cancers ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 3055
Author(s):  
Elisabetta Stanzani ◽  
Leire Pedrosa ◽  
Guillaume Bourmeau ◽  
Oceane Anezo ◽  
Aleix Noguera-Castells ◽  
...  
Keyword(s):  
Cellular Heterogeneity ◽  
In Vitro Assays ◽  
Rna Seq ◽  
Promising Target ◽  
Damage Response ◽  
Integrin Alpha 6 ◽  
And Control ◽  
Improve Patient

Therapeutic resistance after multimodal therapy is the most relevant cause of glioblastoma (GBM) recurrence. Extensive cellular heterogeneity, mainly driven by the presence of GBM stem-like cells (GSCs), strongly correlates with patients’ prognosis and limited response to therapies. Defining the mechanisms that drive stemness and control responsiveness to therapy in a GSC-specific manner is therefore essential. Here we investigated the role of integrin a6 (ITGA6) in controlling stemness and resistance to radiotherapy in proneural and mesenchymal GSCs subtypes. Using cell sorting, gene silencing, RNA-Seq, and in vitro assays, we verified that ITGA6 expression seems crucial for proliferation and stemness of proneural GSCs, while it appears not to be relevant in mesenchymal GSCs under basal conditions. However, when challenged with a fractionated protocol of radiation therapy, comparable to that used in the clinical setting, mesenchymal GSCs were dependent on integrin a6 for survival. Specifically, GSCs with reduced levels of ITGA6 displayed a clear reduction of DNA damage response and perturbation of cell cycle pathways. These data indicate that ITGA6 inhibition is able to overcome the radioresistance of mesenchymal GSCs, while it reduces proliferation and stemness in proneural GSCs. Therefore, integrin a6 controls crucial characteristics across GBM subtypes in GBM heterogeneous biology and thus may represent a promising target to improve patient outcomes.

scholarly journals RgCop-A regularized copula based method for gene selection in single cell rna-seq data

2021 ◽  
Vol 17 (10) ◽  
pp. e1009464
Author(s):  
Snehalika Lall ◽  
Sumanta Ray ◽  
Sanghamitra Bandyopadhyay
Keyword(s):  
Single Cell ◽  
Gene Selection ◽  
Real Life ◽  
Classification Performance ◽  
Rna Seq ◽  
Scale Invariant ◽  
Dependence Measure ◽  
Highly Expressed Genes ◽  
The Stability ◽  
Downstream Analysis

Gene selection in unannotated large single cell RNA sequencing (scRNA-seq) data is important and crucial step in the preliminary step of downstream analysis. The existing approaches are primarily based on high variation (highly variable genes) or significant high expression (highly expressed genes) failed to provide stable and predictive feature set due to technical noise present in the data. Here, we propose RgCop, a novel regularized copula based method for gene selection from large single cell RNA-seq data. RgCop utilizes copula correlation (Ccor), a robust equitable dependence measure that captures multivariate dependency among a set of genes in single cell expression data. We raise an objective function by adding a l1 regularization term with Ccor to penalizes the redundant co-efficient of features/genes, resulting non-redundant effective features/genes set. Results show a significant improvement in the clustering/classification performance of real life scRNA-seq data over the other state-of-the-art. RgCop performs extremely well in capturing dependence among the features of noisy data due to the scale invariant property of copula, thereby improving the stability of the method. Moreover, the differentially expressed (DE) genes identified from the clusters of scRNA-seq data are found to provide an accurate annotation of cells. Finally, the features/genes obtained from RgCop can able to annotate the unknown cells with high accuracy.

scholarly journals Immunolocalization of Na+/K+-ATPase and proliferative activity of enterocytes after administration of glucan in chickens fed T-2 toxin

2018 ◽  
Vol 87 (4) ◽  
pp. 371-377
Author(s):  
Viera Revajová ◽  
Róbert Herich ◽  
Martin Levkut ◽  
Rudolf Žitňan ◽  
Elke Albrecht ◽  
...  
Keyword(s):  
Proliferative Activity ◽  
Positive Influence ◽  
Jejunal Mucosa ◽  
Ion Pump ◽  
Low Doses ◽  
Α Subunit ◽  
Binding Effect ◽  
Dividing Cells ◽  
And Control ◽  
Goblet Cell Density

The protective effect of polysaccharide glucan in chickens fed low doses of T-2 toxin was assessed. The binder effect of β-D-glucan on jejunal mucosa in relation to the expression of Na+/K+-ATPase, proliferative activity of enterocytes and number of goblet cells was investigated. A total of 40 one-day-old chickens were allocated to four groups: control (C), β-D-glucan (G), T-2 toxin (T) and combined β-D-glucan+T-2 toxin (GT). The chickens were individually administrated per os 1.0 mg/bird/day of β-D-glucan derived from Candida albicans on days 11, 12, and 21 of the experiment (totally 3 mg per bird). T-2 toxin at a concentration of 1.45 μg·kg-1 was added to the feed from day 14 to day 28 of the experiment. The α subunit-specific anti-Na+/K+-ATPase antibody was used to identify the protein by immunofluorescence in the cell membrane of jejunal enterocytes. Higher expression of Na+/K+-ATPase was found in the jejunal epithelial cells and lamina propria in the chickens fed T-2 toxin and administered glucan (P < 0.05) compared to control. The number of proliferated enterocytes was higher in group T compared to group G and control (P < 0.001), as well group GT (P < 0.01). Goblet cell density did not present significant differences between groups of chickens, but group G showed the highest values. These data suggest that administration of pure T-2 toxin at low doses affects primarily the protein synthesis of actively dividing cells. Higher distribution of Na+/K+-ATPase in enterocytes of chickens in GT group suggests positive influence of glucan and mycotoxin on the ion pump. A binding effect of this immunomodulator on the digestive tract mucosa in the applied setup was not observed.

Dickeya solani (black leg disease of potato).

2021 ◽  
Author(s):  
Gerry Saddler
Keyword(s):  
Bacterial Pathogen ◽  
Potato Production ◽  
Northern Europe ◽  
Varietal Resistance ◽  
Seed Certification ◽  
Horticultural Crops ◽  
System P ◽  
Recent Emergence ◽  
Dickeya Solani ◽  
And Control

Abstract Dickeya solani is a bacterial pathogen of potato thought to have crossed from horticultural crops in Northern Europe in 2005-2006. The earliest reports of disease on potato are from Belgium and the Netherlands, though it is now present in most European countries and Israel. Symptoms range from blackleg to top wilt in the growing plant and soft rotting of tubers. Symptoms are indistinguishable from those caused by Pectobacterium atrosepticum, P. carotovorum, P. parmentieri (formerly P. wasabiae) (Khayi et al., 2016) and D. dianthicola and control is usually reliant on seed certification schemes to mitigate its worst effects. It should be noted that most losses are attributable to the certification process itself though losses as high as 30% have been recorded in crops grown in Israel. There is no evidence of varietal resistance in potato. D. solani is a highly clonal organism highlighting its recent emergence as a pathogen but also the vulnerability of Europe's highly integrated potato production system.

scholarly journals Dysregulation of Placental Functions and Immune Pathways in Complete Hydatidiform Moles

2019 ◽  
Vol 20 (20) ◽  
pp. 4999 ◽  
Author(s):  
Jennifer R. King ◽  
Melissa L. Wilson ◽  
Szabolcs Hetey ◽  
Peter Kiraly ◽  
Koji Matsuo ◽  
...  
Keyword(s):  
Gene Expression ◽  
First Trimester ◽  
Receptor Interaction ◽  
Rna Seq ◽  
Bioinformatics Analyses ◽  
Immune Genes ◽  
Molecular Features ◽  
Immune Pathways ◽  
And Control ◽  
Hydatidiform Moles

Gene expression studies of molar pregnancy have been limited to a small number of candidate loci. We analyzed high-dimensional RNA and protein data to characterize molecular features of complete hydatidiform moles (CHMs) and corresponding pathologic pathways. CHMs and first trimester placentas were collected, histopathologically examined, then flash-frozen or paraffin-embedded. Frozen CHMs and control placentas were subjected to RNA-Seq, with resulting data and published placental RNA-Seq data subjected to bioinformatics analyses. Paraffin-embedded tissues from CHMs and control placentas were used for tissue microarray (TMA) construction, immunohistochemistry, and immunoscoring for galectin-14. Of the 14,022 protein-coding genes expressed in all samples, 3,729 were differentially expressed (DE) in CHMs, of which 72% were up-regulated. DE genes were enriched in placenta-specific genes (OR = 1.88, p = 0.0001), of which 79% were down-regulated, imprinted genes (OR = 2.38, p = 1.54 × 10−6), and immune genes (OR = 1.82, p = 7.34 × 10−18), of which 73% were up-regulated. DNA methylation-related enzymes and histone demethylases were dysregulated. “Cytokine–cytokine receptor interaction” was the most impacted of 38 dysregulated pathways, among which 17 were immune-related pathways. TMA-based immunoscoring validated the lower expression of galectin-14 in CHM. In conclusion, placental functions were down-regulated, imprinted gene expression was altered, and immune pathways were activated, indicating complex dysregulation of placental developmental and immune processes in CHMs.

scholarly journals Lethal and sublethal effects of azadirachtin on the bumblebee Bombus terrestris (Hymenoptera: Apidae)

Ecotoxicology ◽  
2014 ◽  
Vol 24 (1) ◽  
pp. 130-142 ◽  
Author(s):  
Wagner Faria Barbosa ◽  
Laurens De Meyer ◽  
Raul Narciso C. Guedes ◽  
Guy Smagghe
Keyword(s):  
Sublethal Effects ◽  
Bombus Terrestris
Sign in / Sign up

Export Citation Format

Share Document