PSVIII-25 Transcriptional reprogramming in rumen epithelium during the developmental transition of pre-ruminant to the ruminant in cattle

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 355-356
Author(s):  
Ransom L Baldwin ◽  
Erin E Connor ◽  
Timothy G Ramsay ◽  
George E Liu ◽  
Cong-Jun Li
Keyword(s):  
Animal Feed ◽  
Expression Patterns ◽  
Principal Component ◽  
Epithelial Tissue ◽  
Dietary Shift ◽  
Rumen Epithelium ◽  
Transcriptional Reprogramming ◽  
Rumen Development ◽  
Signaling Events ◽  
Ruminal Epithelium

Abstract The rumen is a critical organ mediating nutrient uptake and use in cattle. Healthy rumen development is essential to ensure animal feed efficiency. In this work, we present an analysis of transcriptomic dynamics in rumen epithelium during the transition from pre-rumination to rumination in cattle-fed hay or concentrated diets at weaning (eighteen Holstein bull calves, 3 X 6 groups). These two distinct phases of rumen development and function in cattle are tightly regulated by a series of signaling events and clusters of effectors on key pathways. Our analysis identifies putative signaling events and effectors. Gene activity shifts indicated the transcriptomic reprogramming required to induce developmental changes in ruminal epithelium and functional transitions. A principal component analysis distinguished the temporal expression patterns that clustered separately between pre- and post-weaning groups. A GO-term enrichment analysis reflected functional (physical and metabolic) development of ruminal epithelium and revealed the greatest number of DEGs were enriched in biological processes related to energy metabolism. Canonical pathway and upstream regulator analyses revealed transcription reprogramming with clusters of critical pathways and upstream regulators controlling functional and developmental transitions with no significant differences between hay- and concentrate-fed groups at weaning. The most highly activated transcription factors expressed during the weaning transition were PPARGC1A, INSR, NFE2L2, MYC, MYCN, and PPARA. Overall, the dietary shift from liquid to solid feeds prompted transcriptional reprogramming in rumen epithelial tissue reflecting critical nutrient-gene interactions occurring during the developmental progression of ruminant digestion.

scholarly journals Transcriptional Reprogramming in Rumen Epithelium during the Developmental Transition of Pre-Ruminant to the Ruminant in Cattle

Animals ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 2870
Author(s):  
Ransom L. Baldwin Baldwin ◽  
Mei Liu ◽  
Erin E. Connor ◽  
Timothy G. Ramsay ◽  
George E. Liu ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Bioinformatic Analysis ◽  
Gene Activity ◽  
Differentially Expressed ◽  
Critical Pathways ◽  
Dietary Shift ◽  
Rumen Epithelium ◽  
Transcriptional Reprogramming ◽  
Ruminal Epithelium ◽  
And Function

We present an analysis of transcriptomic dynamics in rumen epithelium of 18 Holstein calves during the transition from pre-rumination to rumination in cattle-fed hay or concentrated diets at weaning. Three calves each were euthanized at 14 and 42 d of age to exemplify preweaning, and six calves each were provided diets of either milk replacer and grass hay or calf starter to introduce weaning. The two distinct phases of rumen development and function in cattle are tightly regulated by a series of signaling events and clusters of effectors on critical pathways. The dietary shift from liquid to solid feeds prompted the shifting of gene activity. The number of differentially expressed genes increased significantly after weaning. Bioinformatic analysis revealed gene activity shifts underline the functional transitions in the ruminal epithelium and signify the transcriptomic reprogramming. Gene ontogeny (GO) term enrichment shows extensively activated biological functions of differentially expressed genes in the ruminal epithelium after weaning were predominant metabolic functions. The transcriptomic reprogramming signifies a correlation between gene activity and changes in metabolism and energy production in the rumen epithelium, which occur at weaning when transitioning from glucose use to VFA use by epithelium during the weaning.

Insights into the heat-responsive transcriptional network of tomato contrasting genotypes

2021 ◽  
Vol 19 (1) ◽  
pp. 44-57
Author(s):  
Sirine Werghi ◽  
Charfeddine Gharsallah ◽  
Nishi Kant Bhardwaj ◽  
Hatem Fakhfakh ◽  
Faten Gorsane
Keyword(s):  
Heat Stress ◽  
Heat Shock ◽  
Candidate Genes ◽  
Expression Patterns ◽  
Response Strategies ◽  
Transcriptional Reprogramming ◽  
Genes Encoding ◽  
Breeding Programmes ◽  
Gene Transcripts ◽  
Resource Data

AbstractDuring recent decades, global warming has intensified, altering crop growth, development and survival. To overcome changes in their environment, plants undergo transcriptional reprogramming to activate stress response strategies/pathways. To evaluate the genetic bases of the response to heat stress, Conserved DNA-derived Polymorphism (CDDP) markers were applied across tomato genome of eight cultivars. Despite scattered genotypes, cluster analysis allowed two neighbouring panels to be discriminate. Tomato CDDP-genotypic and visual phenotypic assortment permitted the selection of two contrasting heat-tolerant and heat-sensitive cultivars. Further analysis explored differential expression in transcript levels of genes, encoding heat shock transcription factors (HSFs, HsfA1, HsfA2, HsfB1), members of the heat shock protein (HSP) family (HSP101, HSP17, HSP90) and ascorbate peroxidase (APX) enzymes (APX1, APX2). Based on discriminating CDDP-markers, a protein functional network was built allowing prediction of candidate genes and their regulating miRNA. Expression patterns analysis revealed that miR156d and miR397 were heat-responsive showing a typical inverse relation with the abundance of their target gene transcripts. Heat stress is inducing a set of candidate genes, whose expression seems to be modulated through a complex regulatory network. Integrating genetic resource data is required for identifying valuable tomato genotypes that can be considered in marker-assisted breeding programmes to improve tomato heat tolerance.

scholarly journals Comprehensive Comparison of Amnion Stromal Cells and Chorion Stromal Cells by RNA-Seq

2021 ◽  
Vol 22 (4) ◽  
pp. 1901
Author(s):  
Brielle Jones ◽  
Chaoyang Li ◽  
Min Sung Park ◽  
Anne Lerch ◽  
Vimal Jacob ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stromal Cells ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Principal Component ◽  
Differentially Expressed ◽  
Inflammatory Factor ◽  
Next Generation Sequencing Technology ◽  
Angiogenic Potential ◽  
Anti Inflammatory

Mesenchymal stromal cells derived from the fetal placenta, composed of an amnion membrane, chorion membrane, and umbilical cord, have emerged as promising sources for regenerative medicine. Here, we used next-generation sequencing technology to comprehensively compare amniotic stromal cells (ASCs) with chorionic stromal cells (CSCs) at the molecular and signaling levels. Principal component analysis showed a clear dichotomy of gene expression profiles between ASCs and CSCs. Unsupervised hierarchical clustering confirmed that the biological repeats of ASCs and CSCs were able to respectively group together. Supervised analysis identified differentially expressed genes, such as LMO3, HOXA11, and HOXA13, and differentially expressed isoforms, such as CXCL6 and HGF. Gene Ontology (GO) analysis showed that the GO terms of the extracellular matrix, angiogenesis, and cell adhesion were significantly enriched in CSCs. We further explored the factors associated with inflammation and angiogenesis using a multiplex assay. In comparison with ASCs, CSCs secreted higher levels of angiogenic factors, including angiogenin, VEGFA, HGF, and bFGF. The results of a tube formation assay proved that CSCs exhibited a strong angiogenic function. However, ASCs secreted two-fold more of an anti-inflammatory factor, TSG-6, than CSCs. In conclusion, our study demonstrated the differential gene expression patterns between ASCs and CSCs. CSCs have superior angiogenic potential, whereas ASCs exhibit increased anti-inflammatory properties.

scholarly journals Transcriptional and Physiological Analyses to Assess the Effects of a Novel Biostimulant in Tomato

2022 ◽  
Vol 12 ◽  
Author(s):  
Maria Cristina Della Lucia ◽  
Ali Baghdadi ◽  
Francesca Mangione ◽  
Matteo Borella ◽  
Walter Zegada-Lizarazu ◽  
...  
Keyword(s):  
Water Stress ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Principal Component ◽  
Negative Effects ◽  
Nutrient Metabolism ◽  
Tomato Plants ◽  
Reverse Transcription Pcr ◽  
Osmotic Stress Tolerance

This work aimed to study the effects in tomato (Solanum lycopersicum L.) of foliar applications of a novel calcium-based biostimulant (SOB01) using an omics approach involving transcriptomics and physiological profiling. A calcium-chloride fertilizer (SOB02) was used as a product reference standard. Plants were grown under well-watered (WW) and water stress (WS) conditions in a growth chamber. We firstly compared the transcriptome profile of treated and untreated tomato plants using the software RStudio. Totally, 968 and 1,657 differentially expressed genes (DEGs) (adj-p-value < 0.1 and |log2(fold change)| ≥ 1) were identified after SOB01 and SOB02 leaf treatments, respectively. Expression patterns of 9 DEGs involved in nutrient metabolism and osmotic stress tolerance were validated by real-time quantitative reverse transcription PCR (RT-qPCR) analysis. Principal component analysis (PCA) on RT-qPCR results highlighted that the gene expression profiles after SOB01 treatment in different water regimes were clustering together, suggesting that the expression pattern of the analyzed genes in well water and water stress plants was similar in the presence of SOB01 treatment. Physiological analyses demonstrated that the biostimulant application increased the photosynthetic rate and the chlorophyll content under water deficiency compared to the standard fertilizer and led to a higher yield in terms of fruit dry matter and a reduction in the number of cracked fruits. In conclusion, transcriptome and physiological profiling provided comprehensive information on the biostimulant effects highlighting that SOB01 applications improved the ability of the tomato plants to mitigate the negative effects of water stress.

scholarly journals Distinct gene expression patterns in vector-residing Leishmania infantum identify parasite stage-enriched markers

2019 ◽  
Author(s):  
Iliano V. Coutinho-Abreu ◽  
Tiago D. Serafim ◽  
Claudio Meneses ◽  
Shaden Kamhawi ◽  
Fabiano Oliveira ◽  
...  
Keyword(s):  
Leishmania Infantum ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Principal Component ◽  
Sand Fly ◽  
Parasite Development ◽  
Lutzomyia Longipalpis ◽  
Specific Marker ◽  
Limited Information ◽  
Natural Sand

AbstractPromastigotes of Leishmania infantum undergo a series of extracellular developmental stages inside the natural sand fly vector Lutzomyia longipalpis to reach the infectious stage, the metacyclic promastigote. There is limited information regarding the expression profile of L. infantum developmental stages inside the sand fly vector, and molecular markers that can distinguish the different parasite stages are lacking. We performed RNAseq on unaltered midguts of the sand fly Lutzomyia longipalpis after infection with L. infantum parasites. RNAseq was carried out at various time points throughout parasite development. Principal component analysis mapped the sequences corresponding to the procyclic, nectomonad, leptomonad or metacyclic promastigote stage into distinct positions, with the procyclic stage being the most divergent population. Transcriptional levels across genes varied on average between 10- to 100-fold. Comparison between procyclic and nectomonad promastigotes resulted in 836 differentially expressed (DE) genes; between nectomonad and leptomonad promastigotes in 113 DE genes; and between leptomonad and metacyclic promastigotes in 302 DE genes. Most of the DE genes do not overlap across stages, highlighting the uniqueness of each stage. Furthermore, the different stages of Leishmania parasites exhibited specific transcriptional enrichment across chromosomes. Using the transcriptional signatures exhibited by distinct Leishmania stages during their development in the sand fly midgut, we determined the genes predominantly enriched in each stage, identifying multiple stage-specific markers for L. Infantum. Leading stage-specific marker candidates include genes encoding a zinc transporter in procyclics, a beta-fructofuranidase in nectomonads, a surface antigen-like protein in leptomonads, and an amastin-like surface protein in metacyclics. Overall, these findings demonstrate the transcriptional plasticity of the Leishmania parasite inside the sand fly vector and provide a repertoire of stage-specific markers for further development as molecular tools for epidemiological studies.

scholarly journals Identification of Split-GAL4 Drivers and Enhancers That Allow Regional Cell Type Manipulations of the Drosophila melanogaster Intestine

Genetics ◽  
2020 ◽  
Vol 216 (4) ◽  
pp. 891-903
Author(s):  
Ishara S. Ariyapala ◽  
Jessica M. Holsopple ◽  
Ellen M. Popodi ◽  
Dalton G. Hartwick ◽  
Lily Kahsai ◽  
...  
Keyword(s):  
Gene Expression ◽  
Progenitor Cells ◽  
Expression Patterns ◽  
Cell Types ◽  
Enteroendocrine Cells ◽  
Epithelial Tissue ◽  
Cell Type ◽  
Cell Functions ◽  
Distinct Subset ◽  
Targeted Gene Expression

The Drosophila adult midgut is a model epithelial tissue composed of a few major cell types with distinct regional identities. One of the limitations to its analysis is the lack of tools to manipulate gene expression based on these regional identities. To overcome this obstacle, we applied the intersectional split-GAL4 system to the adult midgut and report 653 driver combinations that label cells by region and cell type. We first identified 424 split-GAL4 drivers with midgut expression from ∼7300 drivers screened, and then evaluated the expression patterns of each of these 424 when paired with three reference drivers that report activity specifically in progenitor cells, enteroendocrine cells, or enterocytes. We also evaluated a subset of the drivers expressed in progenitor cells for expression in enteroblasts using another reference driver. We show that driver combinations can define novel cell populations by identifying a driver that marks a distinct subset of enteroendocrine cells expressing genes usually associated with progenitor cells. The regional cell type patterns associated with the entire set of driver combinations are documented in a freely available website, providing information for the design of thousands of additional driver combinations to experimentally manipulate small subsets of intestinal cells. In addition, we show that intestinal enhancers identified with the split-GAL4 system can confer equivalent expression patterns on other transgenic reporters. Altogether, the resource reported here will enable more precisely targeted gene expression for studying intestinal processes, epithelial cell functions, and diseases affecting self-renewing tissues.

scholarly journals Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift

2019 ◽  
Vol 116 (27) ◽  
pp. 13446-13451 ◽  
Author(s):  
David C. Rinker ◽  
Natalya K. Specian ◽  
Shu Zhao ◽  
John G. Gibbons
Keyword(s):  
Copy Number ◽  
Polar Bear ◽  
Ursus Arctos ◽  
Gene Copy Number ◽  
Brown Bear ◽  
Principal Component ◽  
Ecological Adaptation ◽  
Gene Copy ◽  
Evolutionary Mechanisms ◽  
Dietary Shift

Polar bear (Ursus maritimus) and brown bear (Ursus arctos) are recently diverged species that inhabit vastly differing habitats. Thus, analysis of the polar bear and brown bear genomes represents a unique opportunity to investigate the evolutionary mechanisms and genetic underpinnings of rapid ecological adaptation in mammals. Copy number (CN) differences in genomic regions between closely related species can underlie adaptive phenotypes and this form of genetic variation has not been explored in the context of polar bear evolution. Here, we analyzed the CN profiles of 17 polar bears, 9 brown bears, and 2 black bears (Ursus americanus). We identified an average of 318 genes per individual that showed evidence of CN variation (CNV). Nearly 200 genes displayed species-specific CN differences between polar bear and brown bear species. Principal component analysis of gene CN provides strong evidence that CNV evolved rapidly in the polar bear lineage and mainly resulted in CN loss. Olfactory receptors composed 47% of CN differentiated genes, with the majority of these genes being at lower CN in the polar bear. Additionally, we found significantly fewer copies of several genes involved in fatty acid metabolism as well asAMY1B, the salivary amylase-encoding gene in the polar bear. These results suggest that natural selection shaped patterns of CNV in response to the transition from an omnivorous to primarily carnivorous diet during polar bear evolution. Our analyses of CNV shed light on the genomic underpinnings of ecological adaptation during polar bear evolution.

Total Platelet Transcriptomics and Its Network Analysis by RNA-Seq and miRNA-Seq and PCA Application in Essential Thrombocythaemia

2020 ◽  
pp. 1-8
Author(s):  
Kyung Chul Moon ◽  
Jeong-An Gim ◽  
Dae Sik Kim ◽  
Chul Won Choi ◽  
Jung Yoon ◽  
...  
Keyword(s):  
Regulatory Network ◽  
Target Genes ◽  
Thrombus Formation ◽  
Myeloproliferative Neoplasms ◽  
Expression Patterns ◽  
Principal Component ◽  
Inverse Correlation ◽  
Essential Thrombocythaemia ◽  
Aberrant Expression ◽  
Healthy Control

Differentiating the aetiology of thrombocytosis is limited yet crucial in patients with essential thrombocythaemia (ET). MicroRNAs (miRNAs) regulate haematopoiesis and lineage commitment; aberrant expression of miRNAs plays an important role in myeloproliferative neoplasms. However, the miRNA profile has been poorly explored in ET patients compared to patients with reactive thrombocytosis (RT). A total of 9 samples, including 5 ET patient samples, 2 RT patient samples, and 2 healthy control samples, were analysed in this study. We produced 81.43 million reads from transcripts and 59.60 million reads from small RNAs. We generated a comprehensive miRNA-mRNA regulatory network and identified unique 14 miRNA expression patterns associated with ET. Among the 14 miRNAs, miR-1268a was downregulated in ET and showed an inverse correlation with its 8 putative target genes, including genes associated with thrombus formation and platelet activation (<i>CDH6, EHD2, FUT1, KIF26A, LINC00346, PTPRN, SERF1A,</i> and <i>SLC6A9</i>). Principal component analysis (PCA) showed ET and non-ET groups well clustered in space, suggesting each group had a distinctive expression pattern of mRNAs and miRNAs. These results suggest that the significant dysregulation of miR-1268a and its 8 target genes could be a unique expression of platelet mi­RNAs and miRNA/mRNA regulatory network in ET patients.

scholarly journals Identification of split-GAL4 drivers and enhancers that allow regional cell type manipulations of the Drosophila melanogaster intestine

2020 ◽  
Author(s):  
Ishara S. Ariyapala ◽  
Jessica M. Holsopple ◽  
Ellen M. Popodi ◽  
Dalton G. Hartwick ◽  
Lily Kahsai ◽  
...  
Keyword(s):  
Gene Expression ◽  
Progenitor Cells ◽  
Expression Patterns ◽  
Cell Types ◽  
Enteroendocrine Cells ◽  
Epithelial Tissue ◽  
Cell Type ◽  
Cell Functions ◽  
Distinct Subset ◽  
Targeted Gene Expression

ABSTRACTThe Drosophila adult midgut is a model epithelial tissue composed of a few major cell types with distinct regional identities. One of the limitations to its analysis is the lack of tools to manipulate gene expression based on these regional identities. To overcome this obstacle, we applied the intersectional split-GAL4 system to the adult midgut and report 653 driver combinations that label cells by region and cell type. We first identified 424 split-GAL4 drivers with midgut expression from over 7,300 drivers screened, and then evaluated the expression patterns of each of these 424 when paired with three reference drivers that report activity specifically in progenitor cells, enteroendocrine cells, or enterocytes. We also evaluated a subset of the drivers expressed in progenitor cells for expression in enteroblasts using another reference driver. We show that driver combinations can define novel cell populations by identifying a driver that marks a distinct subset of enteroendocrine cells expressing genes usually associated with progenitor cells. The regional cell type patterns associated with the entire set of driver combinations are documented in a freely available website, providing information for the design of thousands of additional driver combinations to experimentally manipulate small subsets of intestinal cells. In addition, we show that intestinal enhancers identified with the split-GAL4 system can confer equivalent expression patterns on other transgenic reporters. Altogether, the resource reported here will enable more precisely targeted gene expression for studying intestinal processes, epithelial cell functions, and diseases affecting self-renewing tissues.

scholarly journals PENDUGAAN KANDUNGAN ENERGI BRUTO TEPUNG IKAN MENGGUNAKAN TEKNOLOGI Near Infrared (NIR) (Prediction of the Gross Energy for Fishmeal using Near Infrared Reflectant (NIR) Technology)

2016 ◽  
Vol 1 (1) ◽  
pp. 33
Author(s):  
Ati Atul Quddus
Keyword(s):  
Standard Error ◽  
Coefficient Of Variation ◽  
Near Infrared ◽  
Animal Feed ◽  
Principal Component Regression ◽  
Principal Component ◽  
Calibration Equation ◽  
Bomb Calorimeter ◽  
Gross Energy ◽  
Pcr Method

Abstrak Penelitian ini bertujuan untuk menduga kandungan energi bruto tepung ikan untuk bahan pakan ternak menggunakan teknologi Near Infrared (NIR). Tepung ikan yang digunakan dalam penelitian ini diperoleh dari poultry shop yang ada di beberapa daerah di Indonesia dan industri pakan ternak. Penelitian ini menggunakan 50 tepung ikan. Tiga puluh lima sampel digunakan untuk kalibrasi, sedangkan 15 sampel digunakan untuk validasi. Pengukuran NIR reflektan menggunakan sistem NIR. Energi bruto diukur menggunakan bomb calorimeter. Data dianalisis dengan menggunakan regresi linier berganda (RLB) dan Principal Component Regression (PCR). Persamaan kalibrasi dari reflektan dianalisis menggunakan 29 panjang gelombang untuk memprediksi energi bruto. Hasil dari validasi menunjukkan akurasi yang tinggi dengan standar eror dan koefisien variasi untuk energi bruto yaitu 6,6 Kkal/Kg dan 0,2%. Persamaan kalibrasi dari metode PCR menggunakan data absorban. Hasil dari validasinya menunjukkan kurang akurasi dengan nilai standar eror dan koefisien variasi yaitu 119,2 Kkal/kg dan 4,16%. Kata kunci : energi bruto, NIR, RLB, PCR Abstract This experiment was aimed to predict gross energy (GE) content of fishmeal by using Near Infrared (NIR) technology. Fishmeal that was used in this experiment was obtained from the poultry shop in several regions in Indonesia and from animal feed industries. This experiment was conducted by using 50 fishmeals. Thirty five samples out of 50 samples fishmeal was used to develop the NIR of calibration and the rest 15 samples was used to test the accuracy of the calibration. NIR reflectant was measured by NIR system. Gross energy was measured by bomb calorimeter. Collected data were analyzed by using multivariate linier regression (MLR) and principal component regression (PCR). Calibration equation of reflectant was analyzed by using 29 wavelengths for predicting GE. The results of the validation indicated high accuracy with standard error and coefficient of variation for GE: SEp = 6.6 Kkal/Kg, CV = 0.2 % . Calibration equation was obtained from PCR method by using absorbent data. The result of the validation indicated less accuracy with standard error and coefficient of variation for GE: SEp = 119.92 Kkal/Kg, CV = 4.16% . Keywords : Gross Energy, Near infrared Reflectant (NIR), fishmeal, Multivariate Linier Regression (MLR), Principal Component Regression (PCR)

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