23 research outputs found
Short‐term effects of planktonic rotifers and cladocerans on phytoplankton of the River Nile
No full textiPSC-Derived Pancreatic Progenitors Lacking FOXA2 Reveal Alterations in miRNA Expression Targeting Key Pancreatic Genes
No full textPoster by Noura Aldous, Ahmed Elsayed, Nehad Alajez, and Essam M. Abdelalim (Hamad Bin Khalifa University)
Background: Generation of pancreatic beta cells from human pluripotent stem cells (hPSCs) is a promising approach for studying diabetes pathogenesis and transplantation therapy. Our recent study showed that FOXA2 is crucial for human alpha and beta cell development during pancreatic islet differentiation. However, whether miRNAs are regulated by FOXA2 or not is largely unknown.
Objective: In this report, we aimed to capture the dysregulated miRNAs associated with the absence of FOXA2 and identify their pancreatic-specific target genes in the iPSC-derived pancreatic progenitors (iPSC-PPs).
Methods: Two different FOXA2 knockout (FOXA2–/–) hiPSC lines were generated using CRISPR/Cas9. FOXA2–/–hiPSCs and their isogenic controls were differentiated into PPs in vitro using our protocol. PPs generated from FOXA2–/–hiPSCs and WT controls were exposed to RNA-sequencing and miRNA-sequencing. Gene ontology (GO) and KEGG pathways analyses were performed on the differentially expressed genes (DEGs). For differentially expressed miRNAs, a fold-change of >2 with a P-value
Results: Transcriptome analysis on FOXA2–/–PPs compared to WT-PPs revealed 1628 down-regulated (Log2 FC 1.0, p 1.0, p
Conclusion: These findings indicate that the expression of FOXA2 during pancreatic islet development is crucial in maintaining the normal expression of the key miRNAs that target pancreatic endocrine TFs.</p
Genome-wide differential expression profiling of long non-coding RNAs (lncRNAs) in pancreatic cells derived from FOXA2-/- iPSCs
No full textPoster by Ahmed K. Elsayed, Nehad M. Alajez, and Essam M. Abdelalim (Hamad Bin Khalifa University)
Background: Our recent studies showed that FOXA2 plays a key role in the development of endocrine and exocrine pancreas. Downregulation of FOXA2 expression during differentiation of induced pluripotent stem cells (iPSCs) into pancreatic islets leads to a significant reduction in α-and β-cell masses. However, whether these changes are associated with alterations in the expression profile of the long non-coding RNAs (lncRNAs) remains unclear.
Objective: the objective of this study is to investigate the alterations in the lncRNA profile and its relationship with the dysregulated mRNAs at the pancreatic progenitors (PPs) and pancreatic islet stages lacking FOXA2.
Methods: Therefore, here, we used our recently established iPSCs lacking FOXA2 (FOXA2-/- iPSCs). we screened the dysregulated lncRNAs in the pancreatic progenitors (PPs) and β-cell stage derived from FOXA2-/- iPSCs in comparison to its control.
Results: PPs and islet cells lacking FOXA2 showed several dysregulated lncRNAs in comparison to controls. Differential expression analysis identified 442 downregulated and 114 upregulated lncRNAs in PPs and 177 downregulated and 59 upregulated in the β-cell stage. Correlation analysis revealed 12 DE-lncRNAs, which were strongly correlated to key downregulated pancreatic genes in both pancreatic progenitors and beta cell stages (MEG3, H19, ZNF667-AS1, LINC00543, LINC00261, AC097639.1, AL035661.1, SLC25A25-AS1, U73166.1, ZNF790-AS1, MNX1-AS2, and AC091563.1).
Conclusion: Our results showed a strong correlation of lncRNAs to several key pancreatic genes and TFs during pancreatic differentiation. Furthermore, these data suggest that the FOXA2-related defective pancreatic islet development is associated with significant alterations in the expression profile of lncRNAs.</p
Zooplankton communities in Lake Nasser, Egypt, under the current flood regime, before the construction of Grand Ethiopian Renaissance Dam (GERD)
No full textThis study focuses on changes in zooplankton composition and abundance in Lake Nasser during different flood periods before the construction of the Grand Ethiopian Renaissance Dam (GERD). Field surveys were carried out in August 2016 (flood period), December 2016 (post-flood period), and May 2017 (pre-flood period). Fifteen sampling sites representing five sectors were selected to cover the lake whole area. The results revealed a highly significant difference (p ≤ 0.016) in the density of all identified zooplankton groups among different flood seasons and lake locations. The zooplankton standing crop during the flood was higher, by a factor of approximately 3.7, than that recorded in post-flood and pre-flood periods. Zooplankton was dominated by medium-sized Copepoda, two cyclopoids (Thermocyclops neglectus and Mesocyclops ogunnus) and one calanoid (Thermodiaptomus galebi). The euplanktonic rotifer Keratella cochlearis dominated, during post-flood and pre-flood periods, constituting approximately 83% and 77% of total rotifer densities, respectively. Keratella tropica occurred in greatest density during flood made up 52.6% of total rotifers. Diaphanosoma mongolianum was the main cladoceran during flood and post-flood periods, whereas Ceriodaphnia dubia densities were highest for pre-flood periods. This study found that flood regime affect zooplankton composition and density in Lake Nasser
Rasmea Odeh: The Case of an Indomitable Woman
No full textIn this profile of Rasmea Odeh, JPS examines the case of a Palestinian woman who has been incarcerated in both Israel and the United States. After a decade of confinement in Israel, Odeh was freed in a prisoner exchange in 1979. Following deportation from the occupied Palestinian territories, she became a noted social justice and women's rights organizer, first in Lebanon and Jordan, and later in the U.S., where she built the now over 800-strong Arab Women's Committee of Chicago. In April 2017, Odeh accepted a plea bargain that would lead to her deportation from the United States after a years-long legal battle to overturn a devastating conviction on charges of immigration fraud. Observers, legal experts, and supporters consider the case to “reek of political payback,” in the words of longtime Palestine solidarity activist, author, and academic Angela Davis. Odeh's generosity of spirit, biting wit, and easy smile did not desert her throughout the years that she fought her case. To know Odeh is to be reminded that the work of organizing for social justice is about the collective rather than the individual, and that engagement, relationship building, and trust are the foundations of such work.</jats:p
qF3 Analysis Code
No full textProvided here:
-Scripts for Performing quantitative Fast FLIM FRET (qF3) Analysis. Organized into folders by steps (1-13) to run for each biological replicate (Step1_Replicate_Analysis) and then for all combined replicates (Step2_CombineReps_Analysis).
-script used to calculate G factor (for which our original data can be provided upon request)
-Example Master platemap.
-LICENSE file for all code here.
-Author: Nehad Hirmiz ([email protected])
Instructions:
-Download all files here and extract .Zip.
-Install MATLAB Version R2020a with toolboxes:
Signal Processing, Curve Fitting, Image Processing.
-IFF starting with INO FLIM Hyperspectral data * then contact lead for
INO software package including (Release_r10357 package):
INO FHS Acquisition,
INO_FHS_Analysis,
INO_FHS_Batch Analysis
-Follow instructions to run these codes:
See associated text at Protocol Exchange: Title: “Automated, quantitative Fast FLIM-FRET (qF3): A step-by-step protocol to measure dissociation constants for protein-protein interactions in live-cell screening applications.”
LINK
https://doi.org/10.21203/rs.3.pex-1354/v1
And
Instructional videos:
LINK
https://www.youtube.com/playlist?list=PLUiSJrzzg9voe5sjA57oIbfOLAGIrHXR
Erratum: A scientific report on heat transfer analysis in mixed convection flow of Maxwell fluid over an oscillating vertical plate
No full textScientific Reports 7: Article number: 40147; published online: 15 March 2017; updated: 17 May 2018 In the original version of this Article, the author L. C. C. Dennis was inadvertently omitted from the Author Contributions statement and the Supplementary Information. The Author Contributions statement,</jats:p
Gene expression data analysis identifies multiple deregulated pathways in patients with asthma
No full text©2018 The Author(s).Peer reviewe
Targeted MicroRNA Profiling Reveals That Exendin-4 Modulates the Expression of Several MicroRNAs to Reduce Steatosis in HepG2 Cells
No full textExcess hepatic lipid accumulation is the hallmark of non-alcoholic fatty liver disease (NAFLD), for which no medication is currently approved. However, glucagon-like peptide-1 receptor agonists (GLP-1RAs), already approved for treating type 2 diabetes, have lately emerged as possible treatments. Herein we aim to investigate how the GLP-1RA exendin-4 (Ex-4) affects the microRNA (miRNAs) expression profile using an in vitro model of steatosis. Total RNA, including miRNAs, was isolated from control, steatotic, and Ex-4-treated steatotic cells and used for probing a panel of 799 highly curated miRNAs using NanoString technology. Enrichment pathway analysis was used to find the signaling pathways and cellular functions associated with the differentially expressed miRNAs. Our data shows that Ex-4 reversed the expression of a set of miRNAs. Functional enrichment analysis highlighted many relevant signaling pathways and cellular functions enriched in the differentially expressed miRNAs, including hepatic fibrosis, insulin receptor, PPAR, Wnt/β-Catenin, VEGF, and mTOR receptor signaling pathways, fibrosis of the liver, cirrhosis of the liver, proliferation of hepatic stellate cells, diabetes mellitus, glucose metabolism disorder and proliferation of liver cells. Our findings suggest that miRNAs may play essential roles in the processes driving steatosis reduction in response to GLP-1R agonists, which warrants further functional investigation
Vertical distribution of zooplankton in Lake Nasser
No full textThe composition and distribution of zooplankton communities in three depths (surface, 10–5 m and 20–15 m depths) along main channel of Lake Nasser were studied in 2013. The density of total zooplankton was increased to maximum during winter and autumn at surface water (39,362 and 63,100 Ind. m−3, respectively) and gradually decreased with depth until attaining the lowest average density at 20–15 m (12,460 and 8976 Ind. m−3). During spring and summer, zooplankton was irregularly distributed through the water profile, where the highest average density was recorded at 10–5 m depth (66,007 and 66,734 Ind. m−3). Copepoda was the dominant zooplankton group at all depths, it represented about 70–76.2% of the total zooplankton count. Cladocera formed about 13.4%, 14.5% and 11% of total zooplankton density for surface, 10–5 m and 20–15 m depth. It was decreased with increasing depth during winter and autumn; however it attained its maximum density at 10–5 m depth during spring and summer. Rotifera average density decreased with increasing depth. The dominant zooplankton species inhabiting Lake Nasser were strongly temperature-dependent. The study recommends the introduction of some pelagic fish species to consume the high persistence of zooplankton community at the upper 10 meters of water column
