scholarly journals Differences in the Loin Tenderness of Iberian Pigs Explained through Dissimilarities in Their Transcriptome Expression Profile

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1715
Author(s):  
Miguel Ángel Fernández-Barroso ◽  
Carmen Caraballo ◽  
Luis Silió ◽  
Carmen Rodríguez ◽  
Yolanda Nuñez ◽  
...  
Keyword(s):  
Shear Force ◽  
Biological Pathways ◽  
Longissimus Dorsi ◽  
Biological Processes ◽  
Meat Tenderness ◽  
Rna Seq ◽  
Regulatory Factors ◽  
Expression Of Genes ◽  
Transcriptome Expression ◽  
Functional Analyses

Tenderness is one of the most important meat quality traits and it can be measured through shear force with the Warner–Bratzler test. In the current study, we use the RNA-seq technique to analyze the transcriptome of Longissimus dorsi (LD) muscle in two groups of Iberian pigs (Tough and Tender) divergent for shear force breeding values. We identified 200 annotated differentially expressed genes (DEGs) and 245 newly predicted isoforms. The RNAseq expression results of 10 genes were validated with quantitative PCR (qPCR). Functional analyses showed an enrichment of DE genes in biological processes related to proteolysis (CTSC, RHOD, MYH8, ACTC1, GADD45B, CASQ2, CHRNA9 and ANKRD1), skeletal muscle tissue development (ANKRD1, DMD, FOS and MSTN), lipid metabolism (FABP3 and PPARGC1A) and collagen metabolism (COL14A1). The upstream analysis revealed a total of 11 transcription regulatory factors that could regulate the expression of some DEGs. Among them, IGF1, VGLL3 and PPARG can be highlighted since they regulate the expression of genes involved in biological pathways that could affect tenderness. The experiment revealed a set of candidate genes and regulatory factors suggestive to search polymorphisms that could be incorporated in a breeding program for improving meat tenderness.

scholarly journals Effect of postmortem storage on shear force value and calpain/calpastatin activity in longissimus dorsi muscle of rusa deer (cervus timorensis)

2018 ◽  
Vol 192 ◽  
pp. 03031
Author(s):  
Orapin Jantasaeng ◽  
Kanya Jirajaroenrat ◽  
Kunya Tuntivisoottikul
Keyword(s):  
Shear Force ◽  
Testing Machine ◽  
Longissimus Dorsi ◽  
Meat Production ◽  
Materials Testing ◽  
Meat Tenderness ◽  
Calpain Activity ◽  
Longissimus Dorsi Muscle ◽  
Aging Period ◽  
Effects Of Aging

The objective of this study was to determine the effects of aging period on shear force values and activities of calpain/calpastatin enzymes of the longissimus dorsi (LD) muscle from rusa deer (Cervus timorensis). The shear force values were measured with instron materials testing machine. Results showed that postmortem storage influenced meat tenderness with a highly significant reduction of shear force value from 9.01±0.83 kg/cm2 at day 1 to 4.34±0.10 kg/cm2 at day 21 (P<0.01). Determination of the enzyme activities indicated that the μ-calpain activity decreased significantly from 1.50±0.42 to 0.19±0.28 units/g of meat (P<0.01), whereas m-calpain activity (22.88±9.64 to 16.95±8.34 units/g of meat) and calpastatin activity (9.93±2.37 to 6.82±2.96 units/g of meat) slightly decreased (P>0.05). Shear force values were significant correlated with higher levels of μ-calpain (r=0.915) and m-calpain (r=0.758), respectively. However, the values were not significant related to the calpastatin activity (r=0.462). Therefore, this study confirmed that in the case of rusa deer, μ-calpain is a key factor controlling postmortem meat tenderness compared to m-calpain and calpastatin. The results suggested that storage of the rusa deer meat for 7 days is enough to achieve aging of the LD muscle, which may help to reduce the cost of meat production.

scholarly journals Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes

2020 ◽  
Author(s):  
Chunyan Li ◽  
Xiaoyun He ◽  
Zijun Zhang ◽  
Chunhuan Ren ◽  
Mingxing Chu
Keyword(s):  
Pineal Gland ◽  
Target Genes ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Biological Processes ◽  
Rna Seq ◽  
Non Coding Rna ◽  
Important Regulator ◽  
Gsh Metabolism ◽  
Transcriptome Expression

Abstract Backgroundlong non-coding RNA (lncRNA) has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, there is little report about lncRNA in pineal gland of sheep. Herein, RNA-Seq was used to detect transcriptome expression pattern in pineal gland between follicular phase (FP) and luteal phase (LP) in FecB BB (MM) and FecB ++ (ww) STH sheep, respectively, and differentially expressed (DE) lncRNAs and mRNAs associated with reproduction were identified.ResultsOverall, 135 DE lncRNAs and 1,360 DE mRNAs in pineal gland between MM and ww sheep were screened. Wherein, 39 DE lncRNAs and 764 DE mRNAs were identified (FP vs LP) in MM sheep, 96 DE lncRNAs and 596 DE mRNAs were identified (FP vs LP) in ww sheep. Moreover, GO and KEGG enrichment analysis indicated that the targets of DE lncRNAs and DE mRNAs were annotated to multiple biological processes such as phototransduction, circadian rhythm, melanogenesis, GSH metabolism and steroid biosynthesis, which directly or indirectly participate in hormone activities to affect sheep reproductive performance. Additionally, co-expression of lncRNAs-mRNAs and the network construction were performed based on correlation analysis, DE lncRNAs can modulate target genes involved in related pathways to affect sheep fecundity. Specifically, like XLOC_466330 , XLOC_532771 , XLOC_028449 targeting RRM2B and GSTK1 , XLOC_391199 targeting STMN1 , XLOC_503926 targeting RAG2 , XLOC_187711 targeting DLG4 were included.ConclusionAll of these differential lncRNAs and mRNAs expression profiles in pineal gland provide a novel resource for elucidating regulatory mechanism underlying STH sheep prolificacy.

scholarly journals Meat Texture Profile and Cutting Strength Analyses of Pork Depending on Breed and Age

2020 ◽  
Vol 20 (2) ◽  
pp. 677-692
Author(s):  
Władysław Migdał ◽  
Marian Różycki ◽  
Aurelia Mucha ◽  
Mirosław Tyra ◽  
Małgorzata Natonek-Wiśniewska ◽  
...  
Keyword(s):  
Shear Force ◽  
Longissimus Dorsi ◽  
Final Decision ◽  
Meat Tenderness ◽  
Technological Properties ◽  
Large White ◽  
Texture Profile ◽  
Texture Parameters ◽  
Slaughter Age ◽  
Imf Content

AbstractThe chemical composition and culinary meat tenderness belong to the most important characteristics determining meat quality and value. The aim of this work was to compare texture profiles and shear force of pork loin (m. longissimus dorsi) and of pork ham (m. semimembranosus) from fatteners of Polish Landrace (PL), Polish Large White (PLW), Duroc, Pietrain and Puławska pig breeds slaughtered at 60, 90, 120, 150, 180 and 210 d of breeding. Meat was roasted at 180°C to inner temperature of 78°C. The intramuscular fat (IMF) content in loin was growing with fattener age (from 1.17% at 60 d to 1.84% at 180 d of life). Between breeds IMF ranged from 0.82% in PLW to 2.29% in Puławska breed. The shear force for loin muscle ranged from 3.42 kG/cm2 at 60 d to 6.54 kG/cm2 at 210 d of life while for and ham muscle 4.4 kG/cm2 at 60 d to 6.78 kG/cm2 at 210 d of life. The hardness (TPA) ranged from 72.29 N at 90 d of life to 109.46 N at 210 d of life. The shear force of loin and ham meat was increasing with age of fatteners and some texture parameters – hardness and chewiness. Nevertheless it seems that the age of 150 days is the time when meat of fatteners is characterized by the highest technological properties. However, the final decision regarding slaughter age should be made taking into account the technological destination of the carcasses. No significant interactions between the animal breed and their age were found for the parameters analysed.

scholarly journals PSII-22 Comparison of the meat quality traits of crossbred pigs and the Large Black pigs

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 241-242
Author(s):  
Yongjie Wang ◽  
Keshari Thakali ◽  
Sarah Shelby ◽  
Jason Apple ◽  
Yan Huang
Keyword(s):  
Meat Quality ◽  
Genomic Diversity ◽  
Longissimus Dorsi ◽  
Rna Seq ◽  
Longissimus Dorsi Muscle ◽  
A Value ◽  
Dorsi Muscle ◽  
Body Weights ◽  
C Value ◽  
Crossbred Pigs

Abstract The purpose of this study was to compare the meat quality and genomic differences between cross-bred commercial pig (CP) and domestic Large Black pig (BP). Seven cross-bred commercial pigs and eight British Large Black pigs were assigned to CP group and BP group, with initial mean body weights of 18.82±1.412 kg for CP group and 23.31±1.935 kg for BP group, P = 0.061, and fed ad libitum. The final BW of the CP at d101 was similar to the BP (130.0±8.16 kg vs. 121.1±2.80 kg, P = 0.132). However, the BP group took 108 days to reach the final BW. The ADG in the CP was higher than BP (1.102±0.0599 kg vs. 0.905±0.0138 kg, P = 0.003). The hot carcass weight of CP was higher (P &lt; 0.01) than BP, but the backfat of BP was higher (P &lt; 0.01) than CP. The a* value of CP was higher (P &lt; 0.05) than BP, and the c* value of CP was tended to be higher (P &lt; 0.10) than BP. However, the h value of BP was higher (P &lt; 0.05) than CP. The longissimus dorsi muscle fat content of BP was higher (P &lt; 0.05) than CP. For the fatty acid composition, the SFA and MUFA of BP were higher (P &lt; 0.05) than CP, but the PUFA of CP was higher (P &lt; 0.05) than BP. The metmyoglobin content of CP was tended to be higher (P &lt; 0.10) than BP. For the meat metabolism, the oxygen consumption of longissimus dorsi muscle of BP was higher (P &lt; 0.01) than CP. The RNA-Seq data showed that the expression of the genes related to lipid metabolism is higher in BP (fold change &gt; 3, P &lt; 0.05). To conclude, BP has higher meat quality, while CP has its advantages in growth performance. And the differences between these two breeds may due to the genomic diversity.

scholarly journals Rewired Pathways and Disrupted Pathway Crosstalk in Schizophrenia Transcriptomes by Multiple Differential Coexpression Methods

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 665
Author(s):  
Hui Yu ◽  
Yan Guo ◽  
Jingchun Chen ◽  
Xiangning Chen ◽  
Peilin Jia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Focal Adhesion ◽  
Biological Pathways ◽  
Postmortem Brain ◽  
Rna Seq ◽  
Hub Genes ◽  
Differential Coexpression ◽  
Pathway Crosstalk ◽  
Microarray Datasets ◽  
Transcriptomic Studies

Transcriptomic studies of mental disorders using the human brain tissues have been limited, and gene expression signatures in schizophrenia (SCZ) remain elusive. In this study, we applied three differential co-expression methods to analyze five transcriptomic datasets (three RNA-Seq and two microarray datasets) derived from SCZ and matched normal postmortem brain samples. We aimed to uncover biological pathways where internal correlation structure was rewired or inter-coordination was disrupted in SCZ. In total, we identified 60 rewired pathways, many of which were related to neurotransmitter, synapse, immune, and cell adhesion. We found the hub genes, which were on the center of rewired pathways, were highly mutually consistent among the five datasets. The combinatory list of 92 hub genes was generally multi-functional, suggesting their complex and dynamic roles in SCZ pathophysiology. In our constructed pathway crosstalk network, we found “Clostridium neurotoxicity” and “signaling events mediated by focal adhesion kinase” had the highest interactions. We further identified disconnected gene links underlying the disrupted pathway crosstalk. Among them, four gene pairs (PAK1:SYT1, PAK1:RFC5, DCTN1:STX1A, and GRIA1:MAP2K4) were normally correlated in universal contexts. In summary, we systematically identified rewired pathways, disrupted pathway crosstalk circuits, and critical genes and gene links in schizophrenia transcriptomes.

scholarly journals The Role of Extracellular Vesicles as Shuttles of RNA and Their Clinical Significance as Biomarkers in Hepatocellular Carcinoma

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 902
Author(s):  
Eva Costanzi ◽  
Carolina Simioni ◽  
Gabriele Varano ◽  
Cinzia Brenna ◽  
Ilaria Conti ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Extracellular Vesicles ◽  
Tumor Metastasis ◽  
Biological Processes ◽  
Rna Molecules ◽  
Expression Of Genes ◽  
Non Coding Rna ◽  
Donor Cells ◽  
Relevant Role

Extracellular vesicles (EVs) have attracted interest as mediators of intercellular communication following the discovery that EVs contain RNA molecules, including non-coding RNA (ncRNA). Growing evidence for the enrichment of peculiar RNA species in specific EV subtypes has been demonstrated. ncRNAs, transferred from donor cells to recipient cells, confer to EVs the feature to regulate the expression of genes involved in differentiation, proliferation, apoptosis, and other biological processes. These multiple actions require accuracy in the isolation of RNA content from EVs and the methodologies used play a relevant role. In liver, EVs play a crucial role in regulating cell–cell communications and several pathophysiological events in the heterogeneous liver class of cells via horizontal transfer of their cargo. This review aims to discuss the rising role of EVs and their ncRNAs content in regulating specific aspects of hepatocellular carcinoma development, including tumorigenesis, angiogenesis, and tumor metastasis. We analyze the progress in EV-ncRNAs’ potential clinical applications as important diagnostic and prognostic biomarkers for liver conditions.

scholarly journals Selection of reference genes for gene expression analysis in Liriodendron hybrids’ somatic embryogenesis and germinative tissues

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tingting Li ◽  
Weigao Yuan ◽  
Shuai Qiu ◽  
Jisen Shi
Keyword(s):  
Gene Expression ◽  
Somatic Embryogenesis ◽  
Reference Genes ◽  
Gene Selection ◽  
Elongation Factor ◽  
Reverse Transcription Pcr ◽  
Expression Of Genes ◽  
Suitable Reference ◽  
Functional Analyses ◽  
Elongation Factor 1

AbstractThe differential expression of genes is crucial for plant somatic embryogenesis (SE), and the accurate quantification of gene expression levels relies on choosing appropriate reference genes. To select the most suitable reference genes for SE studies, 10 commonly used reference genes were examined in synchronized somatic embryogenic and subsequent germinative cultures of Liriodendron hybrids by using quantitative real-time reverse transcription PCR. Four popular normalization algorithms: geNorm, NormFinder, Bestkeeper and Delta-Ct were used to select and validate the suitable reference genes. The results showed that elongation factor 1-gamma, histone H1 linker protein, glyceraldehyde-3-phosphate dehydrogenase and α-tubulin were suitable for SE tissues, while elongation factor 1-gamma and actin were best for the germinative organ tissues. Our work will benefit future studies of gene expression and functional analyses of SE in Liriodendron hybrids. It is also serves as a guide of reference gene selection in early embryonic gene expression analyses for other woody plant species.

scholarly journals Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Chunyan Li ◽  
Xiaoyun He ◽  
Zijun Zhang ◽  
Chunhuan Ren ◽  
Mingxing Chu
Keyword(s):  
Pineal Gland ◽  
Expression Pattern ◽  
Noncoding Rna ◽  
Target Genes ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Rna Seq ◽  
Important Regulator ◽  
Gsh Metabolism ◽  
Transcriptome Expression

Abstract Background Long noncoding RNA (lncRNA) has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, little is known of their expression pattern and potential roles in the pineal gland of sheep. Herein, RNA-Seq was used to detect transcriptome expression pattern in pineal gland between follicular phase (FP) and luteal phase (LP) in FecBBB (MM) and FecB++ (ww) STH sheep, respectively, and differentially expressed (DE) lncRNAs and mRNAs associated with reproduction were identified. Results Overall, 135 DE lncRNAs and 1360 DE mRNAs in pineal gland between MM and ww sheep were screened. Wherein, 39 DE lncRNAs and 764 DE mRNAs were identified (FP vs LP) in MM sheep, 96 DE lncRNAs and 596 DE mRNAs were identified (FP vs LP) in ww sheep. Moreover, GO and KEGG enrichment analysis indicated that the targets of DE lncRNAs and DE mRNAs were annotated to multiple biological processes such as phototransduction, circadian rhythm, melanogenesis, GSH metabolism and steroid biosynthesis, which directly or indirectly participate in hormone activities to affect sheep reproductive performance. Additionally, co-expression of lncRNAs-mRNAs and the network construction were performed based on correlation analysis, DE lncRNAs can modulate target genes involved in related pathways to affect sheep fecundity. Specifically, XLOC_466330, XLOC_532771, XLOC_028449 targeting RRM2B and GSTK1, XLOC_391199 targeting STMN1, XLOC_503926 targeting RAG2, XLOC_187711 targeting DLG4 were included. Conclusion All of these differential lncRNAs and mRNAs expression profiles in pineal gland provide a novel resource for elucidating regulatory mechanism underlying STH sheep prolificacy.

scholarly journals Identification of Potential Key lncRNAs in the Context of Mouse Myeloid Differentiation by Systematic Transcriptomics Analysis

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 630
Author(s):  
Yongqing Lan ◽  
Meng Li ◽  
Shuangli Mi
Keyword(s):  
Transcription Factor ◽  
Cell Model ◽  
Myeloid Differentiation ◽  
Rna Seq ◽  
Hematopoietic Differentiation ◽  
Granulocytic Differentiation ◽  
Expression Of Genes ◽  
Non Coding Rnas

Hematopoietic differentiation is a well-orchestrated process by many regulators such as transcription factor and long non-coding RNAs (lncRNAs). However, due to the large number of lncRNAs and the difficulty in determining their roles, the study of lncRNAs is a considerable challenge in hematopoietic differentiation. Here, through gene co-expression network analysis over RNA-seq data generated from representative types of mouse myeloid cells, we obtained a catalog of potential key lncRNAs in the context of mouse myeloid differentiation. Then, employing a widely used in vitro cell model, we screened a novel lncRNA, named Gdal1 (Granulocytic differentiation associated lncRNA 1), from this list and demonstrated that Gdal1 was required for granulocytic differentiation. Furthermore, knockdown of Cebpe, a principal transcription factor of granulocytic differentiation regulation, led to down-regulation of Gdal1, but not vice versa. In addition, expression of genes involved in myeloid differentiation and its regulation, such as Cebpa, were influenced in Gdal1 knockdown cells with differentiation blockage. We thus systematically identified myeloid differentiation associated lncRNAs and substantiated the identification by investigation of one of these lncRNAs on cellular phenotype and gene regulation levels. This study promotes our understanding of the regulation of myeloid differentiation and the characterization of roles of lncRNAs in hematopoietic system.

Evaluation of period of fasting and mixing of steers prior to slaughter on meat eating quality

2009 ◽  
Vol 2009 ◽  
pp. 138-138
Author(s):  
F O Lively ◽  
B W Moss ◽  
T W J Keady ◽  
L Farmer ◽  
N F S Gault ◽  
...  
Keyword(s):  
Shear Force ◽  
Eating Quality ◽  
Longissimus Dorsi ◽  
Glycogen Depletion ◽  
Meat Eating ◽  
Quadratic Relationship

Mixing of cattle prior to slaughter which results in aggressive activity (Mohan Raj et al 1992) leads to glycogen depletion pre-slaughter and subsequently meat with a higher ultimate pH (pHu). Purchas et al (1990) reported a quadratic relationship between pHu and tenderness with highest shear force values recorded between pHu 5.8 to 6.2. The aim of this study was to determine the effect of fasting and mixing of steers prior to slaughter on the meat eating quality of longissimus dorsi (LD) muscle.

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