scholarly journals Intestinal Transcriptome Analysis Highlights Key Differentially Expressed Genes Involved in Nutrient Metabolism and Digestion in Yellowtail Kingfish (Seriola lalandi) Fed Terrestrial Animal and Plant Proteins

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 621
Author(s):  
Chinh Thi My Dam ◽  
Tomer Ventura ◽  
Mark Booth ◽  
Igor Pirozzi ◽  
Michael Salini ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Raw Materials ◽  
Quantitative Polymerase Chain Reaction ◽  
Nutrient Digestibility ◽  
Differentially Expressed ◽  
Plant Proteins ◽  
Nutrient Metabolism ◽  
Terrestrial Animal ◽  
Yellowtail Kingfish ◽  
Seriola Lalandi

This study investigated the effects of dietary terrestrial animal and plant proteins on the intestinal transcriptomes of yellowtail kingfish (YTK), Seriola lalandi, an ecologically and economically important marine species in Australia. Five diets containing fish meal (FM), poultry by-product meal (PBM), blood meal (BLM), faba bean meal (FBM) and corn gluten meal (CGM) were formulated and fed over a period of 4 weeks. The Illumina RNA-sequencing (RNA-Seq) results identified a suite of differentially expressed genes involved in nutrient metabolism and protein digestion pathways, reinforced by quantitative polymerase chain reaction (qPCR) results. These findings provide molecular support to the notion that PBM and FBM are useful raw materials in commercial diets for YTK. Using the same evidence, we have demonstrated that BLM and CGM may be less useful and their incorporation into commercial aquafeeds for this species should be done cautiously. The differentially expressed genes showed a subtle difference and high correlation with apparent nutrient digestibility of raw materials. Further, our results indicate that transcriptome profiling provides a useful tool to evaluate alternative protein sources for use in aquaculture feeds.

scholarly journals Alternative Feed Raw Materials Modulate Intestinal Microbiota and Its Relationship with Digestibility in Yellowtail Kingfish Seriola lalandi

Fishes ◽  
2020 ◽  
Vol 5 (2) ◽  
pp. 14
Author(s):  
Chinh Thi My Dam ◽  
Mark Booth ◽  
Igor Pirozzi ◽  
Michael Salini ◽  
Richard Smullen ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Raw Materials ◽  
Nutrient Digestibility ◽  
Rrna Gene ◽  
Distal Intestine ◽  
Alternative Feed ◽  
Yellowtail Kingfish ◽  
Seriola Lalandi

Gut microbiota plays a crucial role in nutrient digestibility and fish health. This study aimed to investigate the effects of alternative feed raw materials on the bacterial communities in the distal intestine and its relationship with nutrient digestibility in yellowtail kingfish (YTK), Seriola lalandi. Two 4-week digestibility trials were conducted to evaluate fish meal (FM), two sources of poultry by-product meal (PBM-1 & PBM-2), blood meal (BLM), faba bean meal (FBM), corn gluten meal (CGM), soy protein concentrate (SPC) and wheat flour (WH). The nutrient digestibility value was determined using the stripping fecal collection method. Bacterial communities were characterized by high-throughput sequencing based on V3-V4 region of the 16S rRNA gene. The most abundant phylum identified in the present study was Proteobacteria. A significant change in the distal intestine was observed in fish fed diets containing CGM and BLM, characterized by a reduction of species richness and diversity. Additionally, significant correlation between nutrient digestibility and intestinal microbiota was observed. Allivibrio, Vibrio, Curvibacter, Ruminococcaceae, and Clostridium were positively correlated, whereas Ralstonia genus was negatively correlated with nutrient digestibility. This study demonstrated that intestinal microbiota could be a useful tool for evaluating the digestibility of feed raw materials; however, further culture-based study is needed to confirm this observation.

scholarly journals Identification of Hub Genes in Anaplastic Thyroid Carcinoma: Evidence From Bioinformatics Analysis

2020 ◽  
Vol 19 ◽  
pp. 153303382096213
Author(s):  
Liqi Li ◽  
Mingjie Zhu ◽  
Hu Huang ◽  
Junqiang Wu ◽  
Dong Meng
Keyword(s):  
Thyroid Carcinoma ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Quantitative Polymerase Chain Reaction ◽  
Interaction Network ◽  
Anaplastic Thyroid Carcinoma ◽  
Rank Aggregation ◽  
Differentially Expressed ◽  
Hub Genes ◽  
Rare Type

Anaplastic thyroid carcinoma (ATC) is a rare type of thyroid cancer that results in fatal clinical outcomes; the pathogenesis of this life-threatening disease has yet to be fully elucidated. This study aims to identify the hub genes of ATC that may play key roles in ATC development and could serve as prognostic biomarkers or therapeutic targets. Two microarray datasets (GSE33630 and GSE53072) were obtained from the Gene Expression Omnibus database; these sets included 16 ATC and 49 normal thyroid samples. Differential expression analyses were performed for each dataset, and 420 genes were screened as common differentially expressed genes using the robust rank aggregation method. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were conducted to explore the potential bio-functions of these differentially expressed genes (DEGs). The terms and enriched pathways were primarily associated with cell cycle, cell adhesion, and cancer-related signaling pathways. Furthermore, a protein-protein interaction network of DEG expression products was constructed using Cytoscape. Based on the whole network, we identified 7 hub genes that included CDK1, TOP2A, CDC20, KIF11, CCNA2, NUSAP1, and KIF2C. The expression levels of these hub genes were validated using quantitative polymerase chain reaction analyses of clinical specimens. In conclusion, the present study identified several key genes that are involved in ATC development and provides novel insights into the understanding of the molecular mechanisms of ATC development.

A three-gene expression signature model to predict neo-chemoradiotherapy response of esophageal squamous cell carcinomas.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. e15135-e15135
Author(s):  
Jing Wen ◽  
Hong Yang ◽  
Kongjia Luo ◽  
Yi Hu ◽  
Xu Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prediction Model ◽  
Differentially Expressed Genes ◽  
Predictive Power ◽  
Predictive Accuracy ◽  
Quantitative Polymerase Chain Reaction ◽  
Gene Expression Signature ◽  
Differentially Expressed ◽  
Linear Discriminant ◽  
Crt Response

e15135 Background: Preoperative chemoradiotherapy (CRT) followed by surgery has been proved to improve survival in comparison with surgery alone. However, the outcomes of CRT are heterogeneous, and no clinical or pathological method could prediction CRT response. In this study, we aim to identify mRNA markers for ESCC CRT-response prediction. Methods: Gene expression analyses were performed on pretreatment cancer biopsies from 28 ESCCs who received neoadjuvant CRT and surgery. Surgical specimens were assessed for the pathological response to CRT. The identified differentially expressed genes were validated by real-time quantitative polymerase chain reaction (qPCR), based on which a classifying model was built up by Fisher’s linear discriminant analysis. The predictive power of this model was further assessed in another set of 32 ESCCs. Results: The profiling of the 28 ESCCs identified 10 differentially expressed genes with more than 2-fold changes between pathological complete responsers (pCRs) and less than pCRs (<pCRs), among which 6 genes (LIMCH1, SDPR, Clorf226, SLC9A9, GSTM3, and IGSF10) were down-regulated and 4 genes (MMP9, MMP1, MMP12 and OASL) up-regulated in pCRs versus <pCRs. A prediction model based on qPCR values of 3 genes was built up, Y=-10.388 - 0.343 × MMP1 + 0.642 × LIMCH1 + 0.921 × Clorf226 with a cut-off value of 0.607. It provided a predictive accuracy of 85.7% with leave-one-out cross-validation. Further, the predictive power of this model was validated in another set of 32 ESCCs, among which a predictive accuracy of 81.3% was achieved. Conclusions: The combination of three genes by qPCR identified by microarrays in our study provides possibility for ESCC CRT prediction, which will facilitate individualization of ESCC treatment. Further perspective validation in larger independent cohorts is warranted to fully assess the predictive power of this prediction model.

Apparent digestibility of raw materials by yellowtail kingfish (Seriola lalandi)

Aquaculture ◽  
2019 ◽  
Vol 511 ◽  
pp. 734233 ◽  
Author(s):  
Chinh T.M. Dam ◽  
Abigail Elizur ◽  
Tomer Ventura ◽  
Michael Salini ◽  
Richard Smullen ◽  
...  
Keyword(s):  
Raw Materials ◽  
Apparent Digestibility ◽  
Yellowtail Kingfish ◽  
Seriola Lalandi

scholarly journals Transcriptome Analysis Reveals Dynamic Cultivar-Dependent Patterns of Gene Expression in Potato Spindle Tuber Viroid-Infected Pepper

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2687
Author(s):  
Nikol Hadjieva ◽  
Elena Apostolova ◽  
Vesselin Baev ◽  
Galina Yahubyan ◽  
Mariyana Gozmanova
Keyword(s):  
Gene Expression ◽  
Gene Ontology ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Quantitative Polymerase Chain Reaction ◽  
Potato Spindle Tuber Viroid ◽  
Fine Tuning ◽  
Differentially Expressed ◽  
Gene Ontology Term ◽  
Ontology Term

Potato spindle tuber viroid (PSTVd) infects various plants. PSTVd pathogenesis is associated with interference with the cellular metabolism and defense signaling pathways via direct interaction with host factors or via the transcriptional or post-transcriptional modulation of gene expression. To better understand host defense mechanisms to PSTVd infection, we analyzed the gene expression in two pepper cultivars, Capsicum annuum Kurtovska kapia (KK) and Djulunska shipka (DS), which exhibit mild symptoms of PSTVd infection. Deep sequencing-based transcriptome analysis revealed differential gene expression upon infection, with some genes displaying contrasting expression patterns in KK and DS plants. More genes were downregulated in DS plants upon infection than in KK plants, which could underlie the more severe symptoms seen in DS plants. Gene ontology enrichment analysis revealed that most of the downregulated differentially expressed genes in both cultivars were enriched in the gene ontology term photosynthesis. The genes upregulated in DS plants fell in the biological process of gene ontology term defense response. We validated the expression of six overlapping differentially expressed genes that are involved in photosynthesis, plant hormone signaling, and defense pathways by quantitative polymerase chain reaction. The observed differences in the responses of the two cultivars to PSTVd infection expand the understanding of the fine-tuning of plant gene expression that is needed to overcome the infection.

scholarly journals Global Brain Transcriptome Analysis of a Tpp1 Neuronal Ceroid Lipofuscinoses Mouse Model

ASN NEURO ◽  
2019 ◽  
Vol 11 ◽  
pp. 175909141984339 ◽  
Author(s):  
Miriam S. Domowicz ◽  
Wen-Ching Chan ◽  
Patricia Claudio-Vázquez ◽  
Judith G. Henry ◽  
Christopher B. Ware ◽  
...  
Keyword(s):  
Mouse Model ◽  
Differentially Expressed Genes ◽  
Quantitative Polymerase Chain Reaction ◽  
Differentially Expressed ◽  
Neuronal Ceroid Lipofuscinoses ◽  
Brain Transcriptome ◽  
Transcriptional Changes ◽  
Gene Transcripts ◽  
End Stage ◽  
Global Brain

In humans, homozygous mutations in the TPP1 gene results in loss of tripeptidyl peptidase 1 (TPP1) enzymatic activity, leading to late infantile neuronal ceroid lipofuscinoses disease. Using a mouse model that targets the Tpp1 gene and recapitulates the pathology and clinical features of the human disease, we analyzed end-stage (4 months) transcriptional changes associated with lack of TPP1 activity. Using RNA sequencing technology, Tpp1 expression changes in the forebrain/midbrain and cerebellum of 4-month-old homozygotes were compared with strain-related controls. Transcriptional changes were found in 510 and 1,550 gene transcripts in forebrain/midbrain and cerebellum, respectively, from Tpp1-deficient brain tissues when compared with age-matched controls. Analysis of the differentially expressed genes using the Ingenuity™ pathway software, revealed increased neuroinflammation activity in microglia and astrocytes that could lead to neuronal dysfunction, particularly in the cerebellum. We also observed upregulation in the production of nitric oxide and reactive oxygen species; activation of leukocyte extravasation signals and complement pathways; and downregulation of major transcription factors involved in control of circadian rhythm. Several of these expression changes were confirmed by independent quantitative polymerase chain reaction and histological analysis by mRNA in situ hybridization, which allowed for an in-depth anatomical analysis of the pathology and provided independent confirmation of at least two of the major networks affected in this model. The identification of differentially expressed genes has revealed new lines of investigation for this complex disorder that may lead to novel therapeutic targets.

scholarly journals Microarray and Growth Analyses Identify Differences and Similarities of Early Corn Response to Weeds, Shade, and Nitrogen Stress

Weed Science ◽  
2012 ◽  
Vol 60 (2) ◽  
pp. 158-166 ◽  
Author(s):  
Janet Moriles ◽  
Stephanie Hansen ◽  
David P. Horvath ◽  
Graig Reicks ◽  
David E. Clay ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
Light Stress ◽  
Growth Yield ◽  
Binding Activity ◽  
Differentially Expressed ◽  
Growth And Yield ◽  
Light Competition

Weed interference with crop growth is often attributed to water, nutrient, or light competition; however, specific physiological responses to these stresses are not well described. This study's objective was to compare growth, yield, and gene expression responses of corn to nitrogen (N), low light (40% shade), and weed stresses. Corn vegetative parameters from V2 to V12 stages, yield parameters, and gene expression using transcriptome (2008) and quantitative polymerase chain reaction (qPCR) (2008/09) analyses at V8 were compared among the stresses and with nonstressed corn. N stress did not affect vegetative parameters, although grain yield was reduced by 40% compared with nonstressed plants. Shade, present until V2, reduced biomass and leaf area > 50% at V2, and recovering plants remained smaller than nonstressed plants at V12. However, grain yields of shade-stressed and nonstressed plants were similar, unless shade remained until V8. Weed stress reduced corn growth and yield in 2008 when weeds remained until V6. In 2009, weed stress until V2 reduced corn vegetative growth, but yield reductions occurred only if weed stress remained until V6 or later. Principle component analysis of differentially expressed genes indicated that shade and weed stress had more similar gene expression patterns to each other than they did to nonstressed or N-stressed tissues. However, corn grown in N-stressed conditions shared 252 differentially expressed genes with weed-stressed plants. Ontologies associated with light/photosynthesis, energy conversion, and signaling were down-regulated in response to all three stresses. Shade and weed stress clustered most tightly together, based on gene expression, but shared only three ontologies, O-METHYLTRANSFERASE activity (lignification processes), POLY(U)-BINDING activity (posttranscriptional gene regulation), and stomatal movement. Based on morphologic and genomic observations, weed stress to corn was not explained by individual effects of N or light stress. Therefore, we hypothesize that these stresses share limited signaling mechanisms.

Exploring differentially expressed genes associated with coat color in goat skin using RNA-seq

2019 ◽  
Vol 99 (2) ◽  
pp. 357-366
Author(s):  
Yongdong Peng ◽  
Yaqi Wang ◽  
Ruining Wang ◽  
Liying Geng ◽  
Ruxue Ma ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Quantitative Polymerase Chain Reaction ◽  
Differentially Expressed ◽  
Rna Seq ◽  
White Skin ◽  
Black And White ◽  
Goat Skin ◽  
Skin Physiology ◽  
Black Goat

Fur color in domestic goats is an important, genetically determined characteristic that is associated with economic value. This study was designed to perform a comprehensive expression profiling of genes expressed in the skin tissues from Laiwu Black goat and Lubei White goat. Comparisons of black and white goat skin transcriptomes revealed 102 differentially expressed genes (DEGs), of which 38 were upregulated and 64 downregulated in black skin compared with white skin. Among the DEGs, we identified six genes involved in pigmentation, including agouti signaling protein (ASIP), CAMP responsive element binding protein 3-like 1 (CREB3L1), dopachrome tautomerase (DCT), premelanosome protein (PMEL), transient receptor potential cation channel subfamily M member 1 (TRPM1), and tyrosinase-related protein 1 (TYRP1). Notably, there were no significant differences in the expression of melanocortin 1 receptor, microphthalmia-associated transcription factor, tyrosinase, and KIT proto-oncogene receptor tyrosine kinase between the black and white skin samples, whereas ASIP expression was detected only in white skin. PMEL, TRPM1, TYRP1, and DCT showed higher expression in black goat skin, but ASIP and CREB3L1 had higher expression in white goat skin. Quantitative polymerase chain reaction results for PMEL, TRPM1, DCT, TYRP1, and CREB3L1 expression were consistent with those for RNA-seq. These results will expand our understanding of the complex molecular mechanisms of skin physiology and melanogenesis in goats, and provide a foundation for future studies.

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