RNA-Seq Approach for Genetic Improvement of Meat Quality in Pig and Evolutionary Insight into the Substrate Specificity of Animal Carbonyl Reductases

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 < 0.01) than BP, but the backfat of BP was higher (P < 0.01) than CP. The a* value of CP was higher (P < 0.05) than BP, and the c* value of CP was tended to be higher (P < 0.10) than BP. However, the h value of BP was higher (P < 0.05) than CP. The longissimus dorsi muscle fat content of BP was higher (P < 0.05) than CP. For the fatty acid composition, the SFA and MUFA of BP were higher (P < 0.05) than CP, but the PUFA of CP was higher (P < 0.05) than BP. The metmyoglobin content of CP was tended to be higher (P < 0.10) than BP. For the meat metabolism, the oxygen consumption of longissimus dorsi muscle of BP was higher (P < 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 > 3, P < 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.

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Phenotypic and genetic variation of ultraviolet–visible-infrared spectral wavelengths of bovine meat

Scientific Reports ◽

10.1038/s41598-021-93457-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Giovanni Bittante ◽

Simone Savoia ◽

Alessio Cecchinato ◽

Sara Pegolo ◽

Andrea Albera

Keyword(s):

Meat Quality ◽

Genetic Improvement ◽

Near Infrared ◽

Infrared Region ◽

Phenotypic Variance ◽

Quality Traits ◽

Meat Quality Traits ◽

Infrared Spectral ◽

Portable Spectrometers ◽

Absorbance Spectra

AbstractSpectroscopic predictions can be used for the genetic improvement of meat quality traits in cattle. No information is however available on the genetics of meat absorbance spectra. This research investigated the phenotypic variation and the heritability of meat absorbance spectra at individual wavelengths in the ultraviolet–visible and near-infrared region (UV–Vis-NIR) obtained with portable spectrometers. Five spectra per instrument were taken on the ribeye surface of 1185 Piemontese young bulls from 93 farms (13,182 Herd-Book pedigree relatives). Linear animal model analyses of 1481 single-wavelengths from UV–Vis-NIRS and 125 from Micro-NIRS were carried out separately. In the overlapping regions, the proportions of phenotypic variance explained by batch/date of slaughter (14 ± 6% and 17 ± 7%,), rearing farm (6 ± 2% and 5 ± 3%), and the residual variances (72 ± 10% and 72 ± 5%) were similar for the UV–Vis-NIRS and Micro-NIRS, but additive genetics (7 ± 2% and 4 ± 2%) and heritability (8.3 ± 2.3% vs 5.1 ± 0.6%) were greater with the Micro-NIRS. Heritability was much greater for the visible fraction (25.2 ± 11.4%), especially the violet, blue and green colors, than for the NIR fraction (5.0 ± 8.0%). These results allow a better understanding of the possibility of using the absorbance of visible and infrared wavelengths correlated with meat quality traits for the genetic improvement in beef cattle.

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Assessment of chicken breast shelf life based on bench-top and portable NIR spectroscopy tools coupled with chemometrics

Food Quality and Safety ◽

10.1093/fqsafe/fyaa032 ◽

2020 ◽

Author(s):

Ilaria Lanza ◽

Daniele Conficoni ◽

Stefania Balzan ◽

Marco Cullere ◽

Luca Fasolato ◽

...

Keyword(s):

Discriminant Analysis ◽

Shelf Life ◽

Meat Quality ◽

Near Infrared ◽

Nir Spectroscopy ◽

Life Assessment ◽

Chicken Breast ◽

Portable Devices ◽

Physicochemical Processes ◽

Insight Into

Abstract Near-infrared (NIR) spectroscopy is a rapid technique able to assess meat quality even if its capability to determine the shelf life of chicken fresh cuts is still debated, especially for portable devices. The aim of the study was to compare bench-top and portable NIR instruments in discriminating between four chicken breast refrigeration times (RT), coupled with multivariate classifier models. Ninety-six samples were analysed by both NIR tools at 2, 6, 10 and 14 days post-mortem. NIR data were subsequently submitted to partial least squares discriminant analysis (PLS-DA) and canonical discriminant analysis (CDA). The latter was preceded by double feature selection based on Boruta and Stepwise procedures. PLS-DA sorted moderate separation of RT theses, while shelf life assessment was more accurate on application of Stepwise-CDA. Bench-top tool had better performance than portable one, probably because it captured more informative spectral data as shown by the variable importance in projection (VIP) and restricted pool of Stepwise-CDA predictive scores (SPS). NIR tools coupled with a multivariate model provide deep insight into the physicochemical processes occurring during storage. Spectroscopy showed reliable effectiveness to recognise a 7-day shelf life threshold of breasts, suitable for routine at-line application for screening of meat quality.

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Structural insight into OprD substrate specificity

Nature Structural & Molecular Biology ◽

10.1038/nsmb1304 ◽

2007 ◽

Vol 14 (11) ◽

pp. 1108-1109 ◽

Cited By ~ 66

Author(s):

Shyamasri Biswas ◽

Mohammad M Mohammad ◽

Dimki R Patel ◽

Liviu Movileanu ◽

Bert van den Berg

Keyword(s):

Substrate Specificity ◽

Structural Insight ◽

Insight Into

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A Transcriptomic Analysis of Gonads from the Low-Temperature-Induced Masculinization of Takifugu rubripes

Animals ◽

10.3390/ani11123419 ◽

2021 ◽

Vol 11 (12) ◽

pp. 3419

Author(s):

He Zhou ◽

Yuqing Sun ◽

Xin Li ◽

Ziyu Zhou ◽

Kexin Ma ◽

...

Keyword(s):

Low Temperature ◽

Transcriptome Sequencing ◽

Average Length ◽

Gonadal Development ◽

Temperature Treatment ◽

Takifugu Rubripes ◽

Rna Seq ◽

Low Temperature Treatment ◽

Cultured Fish ◽

Insight Into

The phenotypic sex of fish is usually plastic. Low-temperature treatment induces the masculinization of Takifugu rubripes, resulting in pseudo-males (PM) with the physiological sex of a male (M) and genetic sex of a female (F). For a comparison of gonadal transcriptomes, we collected gonads from three groups of T. rubripes (F, M, and PM) for high-throughput transcriptome sequencing. The results provided 467,640,218 raw reads (70.15 Gb) and a total of 436,151,088 clean reads (65.43 Gb), with an average length of 150 bp. Only 79 differentially expressed genes (DEGs) were identified between F and PM, whereas 12,041 and 11,528 DEGs were identified between F and M, and PM and M, respectively. According to the functional annotation of DEGs, 13 DEGs related to gonadal development were screened (LOC101066759, dgat1, limk1, fbxl3, col6a3, fgfr3, dusp22b, svil, abhd17b, srgap3, tmem88b, bud4, and mustn10) which might participate in formating PM. A quantitative PCR of the DEGs confirmed the reliability of the RNA-seq. Our results provide an important contribution to the genome sequence resources for T. rubripes and insight into the molecular mechanism of masculinization in a cultured fish subject to low-temperature treatment.

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Probing the promiscuity of ent-kaurene oxidases via combinatorial biosynthesis

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1512096113 ◽

2016 ◽

Vol 113 (9) ◽

pp. 2526-2531 ◽

Cited By ~ 27

Author(s):

Sibongile Mafu ◽

Meirong Jia ◽

Jiachen Zi ◽

Dana Morrone ◽

Yisheng Wu ◽

...

Keyword(s):

Natural Products ◽

Metabolic Engineering ◽

Substrate Specificity ◽

Plant Hormone ◽

Structural Similarity ◽

Combinatorial Biosynthesis ◽

Underlying Structure ◽

Engineering System ◽

Insight Into

The substrate specificity of enzymes from natural products’ metabolism is a topic of considerable interest, with potential biotechnological use implicit in the discovery of promiscuous enzymes. However, such studies are often limited by the availability of substrates and authentic standards for identification of the resulting products. Here, a modular metabolic engineering system is used in a combinatorial biosynthetic approach toward alleviating this restriction. In particular, for studies of the multiply reactive cytochrome P450, ent-kaurene oxidase (KO), which is involved in production of the diterpenoid plant hormone gibberellin. Many, but not all, plants make a variety of related diterpenes, whose structural similarity to ent-kaurene makes them potential substrates for KO. Use of combinatorial biosynthesis enabled analysis of more than 20 such potential substrates, as well as structural characterization of 12 resulting unknown products, providing some insight into the underlying structure–function relationships. These results highlight the utility of this approach for investigating the substrate specificity of enzymes from complex natural products’ biosynthesis.

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Comprehensive Analysis of lncRNAs and circRNAs Reveals the Metabolic Specialization in Oxidative and Glycolytic Skeletal Muscles

International Journal of Molecular Sciences ◽

10.3390/ijms20122855 ◽

2019 ◽

Vol 20 (12) ◽

pp. 2855 ◽

Cited By ~ 3

Author(s):

Linyuan Shen ◽

Mailin Gan ◽

Qianzi Tang ◽

Guoqing Tang ◽

Yanzhi Jiang ◽

...

Keyword(s):

Meat Quality ◽

Skeletal Muscles ◽

Target Genes ◽

Fiber Type ◽

Muscle Metabolism ◽

Reduction Process ◽

Differentially Expressed ◽

Rna Seq ◽

Oxidation Reduction ◽

Regulatory Analysis

The biochemical and functional differences between oxidative and glycolytic muscles could affect human muscle health and animal meat quality. However, present understanding of the epigenetic regulation with respect to lncRNAs and circRNAs is rudimentary. Here, porcine oxidative and glycolytic skeletal muscles, which were at the growth curve inflection point, were sampled to survey variant global expression of lncRNAs and circRNAs using RNA-seq. A total of 4046 lncRNAs were identified, including 911 differentially expressed lncRNAs (p < 0.05). The cis-regulatory analysis identified target genes that were enriched for specific GO terms and pathways (p < 0.05), including the oxidation-reduction process, glycolytic process, and fatty acid metabolic. All these were closely related to different phenotypes between oxidative and glycolytic muscles. Additionally, 810 circRNAs were identified, of which 137 were differentially expressed (p < 0.05). Interestingly, some circRNA-miRNA-mRNA networks were found, which were closely linked to muscle fiber-type switching and mitochondria biogenesis in muscles. Furthermore, 44.69%, 39.19%, and 54.01% of differentially expressed mRNAs, lncRNAs, and circRNAs respectively were significantly enriched in pig quantitative trait loci (QTL) regions for growth and meat quality traits. This study reveals a mass of candidate lncRNAs and circRNAs involved in muscle physiological functions, which may improve understanding of muscle metabolism and development from an epigenetic perspective.

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Dysregulated Pyrimidine Biosynthesis Contributes to 5-FU Resistance in SCLC Patient-Derived Organoids but Response to a Novel Polymeric Fluoropyrimidine, CF10

Cancers ◽

10.3390/cancers12040788 ◽

2020 ◽

Vol 12 (4) ◽

pp. 788 ◽

Cited By ~ 3

Author(s):

William H. Gmeiner ◽

Lance D. Miller ◽

Jeff W. Chou ◽

Anthony Dominijanni ◽

Lysette Mutkus ◽

...

Keyword(s):

Drug Target ◽

Pyrimidine Biosynthesis ◽

Cancer Drug ◽

Rna Seq ◽

Novel Approach ◽

Anti Cancer ◽

New Treatments ◽

Insight Into ◽

Sclc Patient ◽

Identify Gene Expression

Chemo-immunotherapy is central to the treatment of small cell lung cancer (SCLC). Despite modest progress made with the addition of immunotherapy, current cytotoxic regimens display minimal survival benefit and new treatments are needed. Thymidylate synthase (TS) is a well-validated anti-cancer drug target, but conventional TS inhibitors display limited clinical efficacy in refractory or recurrent SCLC. We performed RNA-Seq analysis to identify gene expression changes in SCLC biopsy samples to provide mechanistic insight into the potential utility of targeting pyrimidine biosynthesis to treat SCLC. We identified systematic dysregulation of pyrimidine biosynthesis, including elevated TYMS expression that likely contributes to the lack of efficacy for current TS inhibitors in SCLC. We also identified E2F1-3 upregulation in SCLC as a potential driver of TYMS expression that may contribute to tumor aggressiveness. To test if TS inhibition could be a viable strategy for SCLC treatment, we developed patient-derived organoids (PDOs) from human SCLC biopsy samples and used these to evaluate both conventional fluoropyrimidine drugs (e.g., 5-fluorouracil), platinum-based drugs, and CF10, a novel fluoropyrimidine polymer with enhanced TS inhibition activity. PDOs were relatively resistant to 5-FU and while moderately sensitive to the front-line agent cisplatin, were relatively more sensitive to CF10. Our studies demonstrate dysregulated pyrimidine biosynthesis contributes to drug resistance in SCLC and indicate that a novel approach to target these pathways may improve outcomes.

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