scholarly journals Transcriptomic analyses implicate neuronal plasticity and chloride homeostasis in ivermectin resistance and recovery in a parasitic nematode

2021 ◽  
Author(s):  
Roz Laing ◽  
Stephen R Doyle ◽  
Jennifer McIntyre ◽  
Kirsty Maitland ◽  
Alison Morrison ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Gene ◽  
Animal Health ◽  
Gastrointestinal Nematode ◽  
Parasitic Helminths ◽  
F2 Population ◽  
Reference Isolate ◽  
Chloride Homeostasis ◽  
Genetic Cross ◽  
Susceptible Populations

The antiparasitic drug ivermectin plays an essential role in human and animal health globally. However, ivermectin resistance is widespread in veterinary helminths and there are growing concerns of sub-optimal responses to treatment in related helminths of humans. Despite decades of research, the genetic mechanisms underlying ivermectin resistance are poorly understood in parasitic helminths. This reflects significant uncertainty regarding the mode of action of ivermectin in parasitic helminths, and the genetic complexity of these organisms; parasitic helminths have large, rapidly evolving genomes and differences in evolutionary history and genetic background can confound comparisons between resistant and susceptible populations. We undertook a controlled genetic cross of a multi-drug resistant and a susceptible reference isolate of Haemonchus contortus, an economically important gastrointestinal nematode of sheep, and ivermectin-selected the F2 population for comparison with an untreated F2 control. RNA-seq analyses of male and female adults of all populations identified high transcriptomic differentiation between parental isolates, which was significantly reduced in the F2, allowing differences associated specifically with ivermectin resistance to be identified. In all resistant populations, there was constitutive upregulation of a single gene, HCON_00155390:cky-1, a putative pharyngeal-expressed transcription factor, in a narrow locus on chromosome V previously shown to be under ivermectin selection. In addition, we detected sex-specific differences in gene expression between resistant and susceptible populations, including constitutive upregulation of a P-glycoprotein, HCON_00162780:pgp-11, in resistant males only. After ivermectin selection, we identified differential expression of genes with roles in neuronal function and chloride homeostasis, which is consistent with an adaptive response to ivermectin-induced hyperpolarisation of neuromuscular cells. Overall, we show the utility of a genetic cross to identify differences in gene expression that are specific to ivermectin selection and provide a framework to better understand ivermectin resistance and recovery in parasitic helminths.

Linking transcription, RNA polymerase II elongation and alternative splicing

2020 ◽  
Vol 477 (16) ◽  
pp. 3091-3104 ◽  
Author(s):  
Luciana E. Giono ◽  
Alberto R. Kornblihtt
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Rna Polymerase Ii ◽  
Environmental Changes ◽  
Transcription Elongation ◽  
Single Gene ◽  
Regulation Of Gene Expression ◽  
Regulation Of Transcription ◽  
Stepping Stones ◽  
Eukaryotic Transcription

Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.

Stop the new gene, the alien: Predicted breakdown of MYB overexpression by ncRNA mediated gene regulations

2017 ◽  
Vol 4 (2) ◽  
Author(s):  
NEHA SINGH ◽  
INDERJEET BHOGAL ◽  
ABHISHEK KUMAR ◽  
PUNIT TYAGI ◽  
GIRIJA SIKARWAR ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Gene ◽  
Neutral Theory ◽  
Poor Performance ◽  
Warning Sign ◽  
Cellular Mechanisms ◽  
Constitutive Overexpression ◽  
New Gene ◽  
Altered Gene ◽  
Growing Conditions

Acclimatization is a process that occurs in individual cells to a drastic change in micro and macro environments. When an organism is subjected to a new environment or a change in its normal growing conditions, the cellular mechanisms initiate a warning sign and over a period of time or over generations the acquired, modified traits are being communicated and fixed as a new trait. If there is lack of equilibrium within the cell due to over expression of a single gene or network of associated genes either manmade or due to mutations, the organism or plant tries to fix it by initiating gene regulatory mechanisms. According to our neutral theory of gene expression, always a cell tries to maintain its pH by modifying its cytosol through altered gene expression. In the present investigation, 198 AtMYB genes were analyzed and found to play an intrinsic photosystem linked network of 38 nodes where MYB being regulated by a set of 48 miRNAs. Members of the network have evidence-based link to energy related mechanisms. Altering gene expression to an extent where, the cell may not be able to fix it or a trait, which requires excessive energy loss escorts the organism’s gene regulation by breakdown of the introduced sequence over few generations. Events with constitutive overexpression may suffer poor performance over the years based on gene network prevailing in the crop of interest. Hence, network rewiring with minimal energy expenses is concerned.

scholarly journals Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guiomar Martín ◽  
Yamile Márquez ◽  
Federica Mantica ◽  
Paula Duque ◽  
Manuel Irimia
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Alternative Splicing ◽  
Stress Responses ◽  
Target Genes ◽  
Intron Retention ◽  
Single Gene ◽  
Exon Skipping ◽  
Environmental Response ◽  
Biotic Stresses

Abstract Background Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, a comprehensive study contrasting stress-response and tissue-specific AS patterns and directly comparing them with those of animal models is still missing. Results We generate a massive resource for Arabidopsis thaliana, PastDB, comprising AS and gene expression quantifications across tissues, development and environmental conditions, including abiotic and biotic stresses. Harmonized analysis of these datasets reveals that A. thaliana shows high levels of AS, similar to fruitflies, and that, compared to animals, disproportionately uses AS for stress responses. We identify core sets of genes regulated specifically by either AS or transcription upon stresses or among tissues, a regulatory specialization that is tightly mirrored by the genomic features of these genes. Unexpectedly, non-intron retention events, including exon skipping, are overrepresented across regulated AS sets in A. thaliana, being also largely involved in modulating gene expression through NMD and uORF inclusion. Conclusions Non-intron retention events have likely been functionally underrated in plants. AS constitutes a distinct regulatory layer controlling gene expression upon internal and external stimuli whose target genes and master regulators are hardwired at the genomic level to specifically undergo post-transcriptional regulation. Given the higher relevance of AS in the response to different stresses when compared to animals, this molecular hardwiring is likely required for a proper environmental response in A. thaliana.

scholarly journals Equine Genital Squamous Cell Carcinoma Associated with EcPV2 Infection: RANKL Pathway Correlated to Inflammation and Wnt Signaling Activation

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 244
Author(s):  
Samanta Mecocci ◽  
Ilaria Porcellato ◽  
Federico Armando ◽  
Luca Mechelli ◽  
Chiara Brachelente ◽  
...  
Keyword(s):  
Gene Expression ◽  
Wnt Signaling ◽  
Squamous Cell ◽  
Molecular Mechanisms ◽  
Animal Health ◽  
Wnt Signaling Pathway ◽  
Nuclear Factor ◽  
Nuclear Factor Kappa ◽  
Signaling Activation ◽  
Expression Evaluation

Equine genital squamous cell carcinomas (egSCCs) are among the most common equine tumors after sarcoids, severely impairing animal health and welfare. Equus caballus papillomavirus type 2 (EcPV2) infection is often related to these tumors. The aim of this study was to clarify the molecular mechanisms behind egSCCs associated with EcPV2 infection, investigating receptor activator of nuclear factor-kappa B ligand (RANKL) signaling in NF-kB pathway, together with the Wnt and IL17 signaling pathways. We analyzed the innate immune response through gene expression evaluation of key cytokines and transcription factors. Moreover, Ki67 index was assessed with immunohistochemistry. EcPV2-E6 DNA was checked, and viral presence was confirmed in 21 positive out to 23 cases (91%). Oncogene expression was confirmed in 14 cases (60.8%) for E6 and in 8 (34.7%) for E2. RANKL, nuclear factor kappa-light-chain-enhancer of activated B cells (NFKB)-p50, NFKBp65, interleukin (IL)-6, IL17, IL23p19, IL8, IL12p35, IL12p40, β-catenin (BCATN1), FOS like 1 (FOSL1), and lymphoid enhancer binding factor 1 (LEF1) showed a significant upregulation in tumor samples compared to healthy tissues. Our results describe an inflammatory environment characterized by the activation of RANKL/RANK and IL17 with the relative downstream pathways, and a positive modulation of inflammatory cytokines genes such as IL6 and IL8. Moreover, the increase of BCATN1, FOSL1, and LEF1 gene expression suggests an activation of both canonical and non-canonical Wnt signaling pathway that could be critical for carcinogenesis and tumor progression.

Control of cellular gene expression during adenovirus infection: induction and shut-off of dihydrofolate reductase gene expression by adenovirus type 2

1983 ◽  
Vol 3 (5) ◽  
pp. 819-828 ◽  
Author(s):  
S S Yoder ◽  
B L Robberson ◽  
E J Leys ◽  
A G Hook ◽  
M Al-Ubaidi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Synthesis ◽  
Steady State ◽  
Dihydrofolate Reductase ◽  
Relative Rate ◽  
Single Gene ◽  
Adenovirus Type ◽  
Human Cells ◽  
Adenovirus Infection ◽  
Specific Mrna

Infection of human cells by adenovirus results in multiple alterations of host gene expression. To examine the effects of viral infection on the expression of a single gene, a line of human cells was developed which is resistant to growth in methotrexate and which contains amplified RNA and protein specific for dihydrofolate reductase (DHFR). Cytogenetic evidence indicated the presence of amplified DNA. Adenovirus infection of these cells caused an induction and subsequent decline in the synthesis of DHFR protein. The maximum DHFR induction occurred 16 to 19 h after infection and reached a level 2.5-fold greater than that observed in uninfected cells. Induction of DHFR protein synthesis was accompanied by concomitant increases in the level of steady-state DHFR-specific cytoplasmic RNA. The relative rate of DHFR mRNA production (i.e., the appearance of DHFR-specific mRNA sequences in the cytoplasm) also increased 2.5-fold during induction. Later in infection, the relative rate of DHFR protein synthesis declined, reaching a level below that observed in uninfected cells. This decline was accompanied by a similar decline in the steady-state levels of DHFR RNA and in the relative rate of synthesis of DHFR mRNA. These data suggest that adenovirus infection controls DHFR gene expression by increasing and subsequently decreasing the relative rate at which DHFR-specific mRNA sequences appear in the cytoplasm and enter the pool of mRNA available for translation.

scholarly journals Dual gene expression cassette is superior than single gene cassette for enhancing sheath blight tolerance in transgenic rice

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Subhasis Karmakar ◽  
Kutubuddin A. Molla ◽  
Kaushik Das ◽  
Sailendra Nath Sarkar ◽  
Swapan K. Datta ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transgenic Rice ◽  
Single Gene ◽  
Gene Cassette ◽  
Sheath Blight ◽  
Expression Cassette ◽  
Gene Expression Cassette

scholarly journals A probe-based qRT-PCR method to profile immunological gene expression in blood of captive beluga whales (Delphinapterus leucas)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3840 ◽  
Author(s):  
Ming-An Tsai ◽  
I-Hua Chen ◽  
Jiann-Hsiung Wang ◽  
Shih-Jen Chou ◽  
Tsung-Hsien Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune System ◽  
Reference Genes ◽  
Animal Health ◽  
Rna Extraction ◽  
Disease Onset ◽  
Delphinapterus Leucas ◽  
Amplification Efficiency ◽  
Beluga Whales ◽  
Qrt Pcr

Cytokines are fundamental for a functioning immune system, and thus potentially serve as important indicators of animal health. Quantitation of mRNA using quantitative reverse transcription polymerase chain reaction (qRT-PCR) is an established immunological technique. It is particularly suitable for detecting the expression of proteins against which monoclonal antibodies are not available. In this study, we developed a probe-based quantitative gene expression assay for immunological assessment of captive beluga whales (Delphinapterus leucas) that is one of the most common cetacean species on display in aquariums worldwide. Six immunologically relevant genes (IL-2Rα, -4, -10, -12, TNFα, and IFNγ) were selected for analysis, and two validated housekeeping genes (PGK1 and RPL4) with stable expression were used as reference genes. Sixteen blood samples were obtained from four animals with different health conditions and stored in RNAlater™ solution. These samples were used for RNA extraction followed by qRT-PCR analysis. Analysis of gene transcripts was performed by relative quantitation using the comparative Cq method with the integration of amplification efficiency and two reference genes. The expression levels of each gene in the samples from clinically healthy animals were normally distributed. Transcript outliers for IL-2Rα, IL-4, IL-12, TNFα, and IFNγ were noticed in four samples collected from two clinically unhealthy animals. This assay has the potential to identify immune system deviation from normal state, which is caused by health problems. Furthermore, knowing the immune status of captive cetaceans could help both trainers and veterinarians in implementing preventive approaches prior to disease onset.

scholarly journals Convergence of oncogenic cooperation at single-cell and single-gene levels drives leukemic transformation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yuxuan Liu ◽  
Zhimin Gu ◽  
Hui Cao ◽  
Pranita Kaphle ◽  
Junhua Lyu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Cancer Progression ◽  
Single Gene ◽  
Myeloid Cell ◽  
Cellular Level ◽  
Integrative Approach ◽  
Cancer Evolution ◽  
Cell Assays

AbstractCancers develop from the accumulation of somatic mutations, yet it remains unclear how oncogenic lesions cooperate to drive cancer progression. Using a mouse model harboring NRasG12D and EZH2 mutations that recapitulates leukemic progression, we employ single-cell transcriptomic profiling to map cellular composition and gene expression alterations in healthy or diseased bone marrows during leukemogenesis. At cellular level, NRasG12D induces myeloid lineage-biased differentiation and EZH2-deficiency impairs myeloid cell maturation, whereas they cooperate to promote myeloid neoplasms with dysregulated transcriptional programs. At gene level, NRasG12D and EZH2-deficiency independently and synergistically deregulate gene expression. We integrate results from histopathology, leukemia repopulation, and leukemia-initiating cell assays to validate transcriptome-based cellular profiles. We use this resource to relate developmental hierarchies to leukemia phenotypes, evaluate oncogenic cooperation at single-cell and single-gene levels, and identify GEM as a regulator of leukemia-initiating cells. Our studies establish an integrative approach to deconvolute cancer evolution at single-cell resolution in vivo.

Comparison of Gene-Expression of MC3T3-E1 Osteoblastic Cell Cultured on Machined Titanium Surface and Resorbable Blast Material Titanium Surface

2007 ◽  
Vol 361-363 ◽  
pp. 1095-1098
Author(s):  
S.H. Park ◽  
H.H. Kim ◽  
H.S. Lee ◽  
Y.S. Choi ◽  
A.R. Pae ◽  
...  
Keyword(s):  
Gene Expression ◽  
Titanium Surface ◽  
Cell Attachment ◽  
Single Gene ◽  
Rna Extraction ◽  
Genetic Effect ◽  
Osteoblastic Cell ◽  
Machined Surface ◽  
Osteoblastic Cell Line ◽  
Microarray Assay

Because of its high biocompatibility, hydroxyapatite(HA) has been considered as a good blasting material. DNA microarray is a new molecular technology that enables the analysis of gene expression in parallel on a very large number of genes, spanning a significant fraction of the human genome. It is a qualitive analysis (e.g. it can differentiate each single gene) and quantitative, since it has the sensitivity to detect a change of expression level in the investigated cells when compared to normal samples. The aim of this study is to define the cell attachment and the genetic effect of machined surface implant and RBM (resorbable blast media) surface implant on the osteoblastic cell (MC3T3-E1 osteoblastic cell line) by cDNA microarray slide containing 21575 genes. Cells were cultured on machined grade 4 titanium disks(Group 1, machined surface) and disks of RBM (Group 2) and the samples were moved to new dishes and media were added and the plated disks were cultured for 24 hours. Total RNA extraction was performed with Qiagen mini kit (Qiagen, Chatsworth, CA, USA) for microarray assay. Microarray assay after culturing the cells on the machined surface and RBM surface revealed that osteoinductive molecules appeared more prominent on the RBM surface, whereas the adhesion molecules on the biomaterial were higher on the machined surface than RBM surface.

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