Rubia Gallega x Nelore crossbred cattle improve beef tenderness through changes in protein abundance and gene expression

2021 ◽  
pp. 104634
Author(s):  
Adrielle M. Ferrinho ◽  
Gabriella Vespe de Moura ◽  
Taiane da Silva Martins ◽  
Julian Muñoz ◽  
Lenise F. Mueller ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Abundance ◽  
Crossbred Cattle ◽  
Beef Tenderness

scholarly journals Massively parallel gene expression variation measurement of a synonymous codon library

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Alexander Schmitz ◽  
Fuzhong Zhang
Keyword(s):  
Gene Expression ◽  
Codon Usage ◽  
Single Cells ◽  
Massively Parallel ◽  
Protein Abundance ◽  
Translation Efficiency ◽  
Gene Expression Variation ◽  
Expression Variation ◽  
Change In Mean ◽  
Adaptation Index

Abstract Background Cell-to-cell variation in gene expression strongly affects population behavior and is key to multiple biological processes. While codon usage is known to affect ensemble gene expression, how codon usage influences variation in gene expression between single cells is not well understood. Results Here, we used a Sort-seq based massively parallel strategy to quantify gene expression variation from a green fluorescent protein (GFP) library containing synonymous codons in Escherichia coli. We found that sequences containing codons with higher tRNA Adaptation Index (TAI) scores, and higher codon adaptation index (CAI) scores, have higher GFP variance. This trend is not observed for codons with high Normalized Translation Efficiency Index (nTE) scores nor from the free energy of folding of the mRNA secondary structure. GFP noise, or squared coefficient of variance (CV2), scales with mean protein abundance for low-abundant proteins but does not change at high mean protein abundance. Conclusions Our results suggest that the main source of noise for high-abundance proteins is likely not originating at translation elongation. Additionally, the drastic change in mean protein abundance with small changes in protein noise seen from our library implies that codon optimization can be performed without concerning gene expression noise for biotechnology applications.

scholarly journals Myosin Gene Expression and Protein Abundance in Different Castes of the Formosan Subterranean Termite (Coptotermes formosanus)

Insects ◽  
2012 ◽  
Vol 3 (4) ◽  
pp. 1190-1199 ◽  
Author(s):  
Matthew Tarver ◽  
Christopher Florane ◽  
Christopher Mattison ◽  
Beth Holloway ◽  
Alan Lax
Keyword(s):  
Gene Expression ◽  
Coptotermes Formosanus ◽  
Subterranean Termite ◽  
Protein Abundance ◽  
Formosan Subterranean Termite

scholarly journals Effect of Ultimate pH on Postmortem Myofibrillar Protein Degradation and Meat Quality Characteristics of Chinese Yellow Crossbreed Cattle

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Peng Li ◽  
Tiantian Wang ◽  
Yanwei Mao ◽  
Yimin Zhang ◽  
Lebao Niu ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Protein Degradation ◽  
Meat Quality ◽  
Troponin T ◽  
Quality Characteristics ◽  
Myofibrillar Protein ◽  
Cooking Loss ◽  
Crossbred Cattle ◽  
Beef Tenderness ◽  
Fragmentation Index

This paper describes the complex effects of postmortem ultimate pH (pHu) on Chinese Yellow crossbreed cattle quality during postmortem ageing and provides an explanation of how pHu affects beef tenderness. High pHu beef had the highest initial tenderness (P<0.05) compared with other groups at 1 day postmortem. Intermediate and low pHu beef had similar initial WBSF at 1 day postmortem, but intermediate pHu beef had slower tenderization rate than low pHu beef (P<0.05). Purge loss, cooking loss,L*,a*, andb*values decreased with increasing pHu during ageing (P<0.05). Myofibril fragmentation index (MFI) was higher in high pHu beef than intermediate and low pHu beef throughout ageing (P<0.05). Protein degradation studies found that desmin and troponin-T appeared degraded within 0.5 h postmortem for high and low pHu beef, compared to >2 days for intermediate pHu beef. Overall, Chinese Yellow crossbred cattle tenderness is related to pHu, which may be affected by proteolytic enzymatic activity. Therefore, pHu may be used to predict beef tenderness and other quality characteristics during postmortem ageing. To achieve consistent tenderness, different ageing times should be used, depending on pHu.

scholarly journals Feeding strategies alter gene expression of the calpain system and meat quality in the longissimus muscle of Braford steers

2020 ◽  
Vol 33 (5) ◽  
pp. 753-762
Author(s):  
María Sumampa Coria ◽  
Pablo Sebastián Reineri ◽  
Dario Pighin ◽  
Maria Guadalupe Barrionuevo ◽  
Pedro Gabriel Carranza ◽  
...  
Keyword(s):  
Gene Expression ◽  
Shear Force ◽  
Corn Silage ◽  
Feeding Strategies ◽  
Control Group ◽  
Beef Tenderness ◽  
Protein Levels ◽  
Summer Pasture ◽  
Calpain System ◽  
Feeding Systems

Objective: The aim of the present study was to determine the effect of supplementing pasture-finished steers with corn silage on the expression level of the calpain system proteins and beef tenderization.Methods: Thirty Braford steers grazing on summer pasture were used for the study. For 120 days fifteen animals were supplemented with corn silage at 1% of body weight per head per day (Suppl) whereas the remaining 15 steers only received pasture (Contr). Carcass and meat traits were evaluated and compared between groups. Gene expression and activities of proteases (calpain 1 and calpain 2) and inhibitor (calpastatin) were measured using real-time polymerase chain reaction and casein zymography.Results: Carcass and meat traits were significantly different between feeding systems. Supplemented steers showed higher hot carcass weight (p<0.01), fat content (p = 0.02), and Warner-Bratzler shear force (p = 0.03). Furthermore, the control group showed higher protease:inhibitor ratios, at mRNA (p = 0.01) and protein levels (p<0.10). Warner-Bratzler shear force and mRNA calpains:calpastatin ratio were associated in both feeding systems (p<0.01).Conclusion: Based on the results obtained in the study, beef tenderness differences among finishing strategies could be modulated through differential expression of the calpain system proteins.

scholarly journals Disrupted PGR-B and ESR1 signaling underlies defective decidualization linked to severe preeclampsia

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Tamara Garrido-Gomez ◽  
Nerea Castillo-Marco ◽  
Mónica Clemente-Ciscar ◽  
Teresa Cordero ◽  
Irene Muñoz-Blat ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dynamic Network ◽  
Interaction Network ◽  
Global Gene Expression ◽  
Severe Preeclampsia ◽  
Protein Abundance ◽  
Previous Pregnancy ◽  
Global Gene Expression Profiling ◽  
Phd Program

Background:Decidualization of the uterine mucosa drives the maternal adaptation to invasion by the placenta. Appropriate depth of placental invasion is needed to support a healthy pregnancy; shallow invasion is associated with the development of severe preeclampsia (sPE). Maternal contribution to sPE through failed decidualization is an important determinant of placental phenotype. However, the molecular mechanism underlying the in vivo defect linking decidualization to sPE is unknown.Methods:Global RNA sequencing was applied to obtain the transcriptomic profile of endometrial biopsies collected from nonpregnant women who suffer sPE in a previous pregnancy and women who did not develop this condition. Samples were randomized in two cohorts, the training and the test set, to identify the fingerprinting encoding defective decidualization in sPE and its subsequent validation. Gene Ontology enrichment and an interaction network were performed to deepen in pathways impaired by genetic dysregulation in sPE. Finally, the main modulators of decidualization, estrogen receptor 1 (ESR1) and progesterone receptor B (PGR-B), were assessed at the level of gene expression and protein abundance.Results:Here, we discover the footprint encoding this decidualization defect comprising 120 genes—using global gene expression profiling in decidua from women who developed sPE in a previous pregnancy. This signature allowed us to effectively segregate samples into sPE and control groups. ESR1 and PGR were highly interconnected with the dynamic network of the defective decidualization fingerprint. ESR1 and PGR-B gene expression and protein abundance were remarkably disrupted in sPE.Conclusions:Thus, the transcriptomic signature of impaired decidualization implicates dysregulated hormonal signaling in the decidual endometria in women who developed sPE. These findings reveal a potential footprint that could be leveraged for a preconception or early prenatal screening of sPE risk, thus improving prevention and early treatments.Funding:This work has been supported by the grant PI19/01659 (MCIU/AEI/FEDER, UE) from the Spanish Carlos III Institute awarded to TGG. NCM was supported by the PhD program FDGENT/2019/008 from the Spanish Generalitat Valenciana. IMB was supported by the PhD program PRE2019-090770 and funding was provided by the grant RTI2018-094946-B-100 (MCIU/AEI/FEDER, UE) from the Spanish Ministry of Science and Innovation with CS as principal investigator. This research was funded partially by Igenomix S.L.

scholarly journals Proteomic analysis of cell cycle progression in asynchronous cultures, including mitotic subphases, using PRIMMUS

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Tony Ly ◽  
Arlene Whigham ◽  
Rosemary Clarke ◽  
Alejandro J Brenes-Murillo ◽  
Brett Estes ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mass Spectrometry ◽  
Proteomic Analysis ◽  
Cell Cycle Progression ◽  
Protein Abundance ◽  
Phosphorylation Sites ◽  
Mitotic Progression ◽  
Cycle Progression ◽  
Post Translational Modifications ◽  
Temporal Regulation

The temporal regulation of protein abundance and post-translational modifications is a key feature of cell division. Recently, we analysed gene expression and protein abundance changes during interphase under minimally perturbed conditions (Ly et al., 2014, 2015). Here, we show that by using specific intracellular immunolabelling protocols, FACS separation of interphase and mitotic cells, including mitotic subphases, can be combined with proteomic analysis by mass spectrometry. Using this PRIMMUS (PRoteomic analysis of Intracellular iMMUnolabelled cell Subsets) approach, we now compare protein abundance and phosphorylation changes in interphase and mitotic fractions from asynchronously growing human cells. We identify a set of 115 phosphorylation sites increased during G2, termed ‘early risers’. This set includes phosphorylation of S738 on TPX2, which we show is important for TPX2 function and mitotic progression. Further, we use PRIMMUS to provide the first a proteome-wide analysis of protein abundance remodeling between prophase, prometaphase and anaphase.

scholarly journals Differential Gene Expression and Protein Abundance Evince Ontogenetic Bias toward Castes in a Primitively Eusocial Wasp

PLoS ONE ◽  
2010 ◽  
Vol 5 (5) ◽  
pp. e10674 ◽  
Author(s):  
James H. Hunt ◽  
Florian Wolschin ◽  
Michael T. Henshaw ◽  
Thomas C. Newman ◽  
Amy L. Toth ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Protein Abundance ◽  
Primitively Eusocial Wasp ◽  
Eusocial Wasp ◽  
Differential Gene ◽  
Primitively Eusocial

scholarly journals Pseudomonas mRNA 2.0: Boosting Gene Expression Through Enhanced mRNA Stability and Translational Efficiency

2019 ◽  
Author(s):  
Dário Neves ◽  
Stefan Vos ◽  
Lars M. Blank ◽  
Birgitta E. Ebert
Keyword(s):  
Gene Expression ◽  
Mrna Stability ◽  
Expression Cassette ◽  
Translational Efficiency ◽  
Cell Factory ◽  
Transcriptional Level ◽  
Protein Abundance ◽  
Mrna Levels ◽  
Microbial Cell Factory ◽  
Cell Factories

AbstractHigh gene expression of enzymes partaking in recombinant production pathways is a desirable trait among cell factories belonging to all different kingdoms of life. High enzyme abundance is generally aimed for by utilizing strong promoters, which ramp up gene transcription and mRNA levels. Increased protein abundance can alternatively be achieved by optimizing the expression on the post-transcriptional level. Here, we evaluated protein synthesis with a previously proposed optimized gene expression architecture, in which mRNA stability and translation initiation are modulated by genetic parts such as self-cleaving ribozymes and a bicistronic design, which have initially been described to support the standardization of gene expression. The optimized gene expression architecture was tested in Pseudomonas taiwanensis VLB120, a promising, novel microbial cell factory. The expression cassette was employed on a plasmid basis and after single genomic integration. We used three constitutive and two inducible promoters to drive the expression of two fluorescent reporter proteins and a short acetoin biosynthesis pathway. The performance was confronted with that of a traditional expression cassette harboring the same promoter and gene of interest but lacking the genetic parts for increased expression efficiency. The optimized expression cassette granted higher protein abundance independently of the expression basis or promoter used proving its value for applications requiring high protein abundance.

scholarly journals Ordered patterning of the sensory system is susceptible to stochastic features of gene expression

2019 ◽  
Author(s):  
Ritika Giri ◽  
Dimitrios K. Papadopoulos ◽  
Diana M. Posadas ◽  
Hemanth K. Potluri ◽  
Pavel Tomancak ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Fate ◽  
Sensory System ◽  
Intrinsic Noise ◽  
Protein Abundance ◽  
Dependent Manner ◽  
Genomic Locus ◽  
Critical Feature ◽  
Environmental Signals ◽  
Microrna Regulation

AbstractSensory neuron numbers and positions are precisely organized to accurately map environmental signals in the brain. However, this precision must emerge from biochemical processes within and between cells that are stochastic. We measured intrinsic noise in senseless protein output, a key determinant of sensory fate, during Drosophila development. Perturbing microRNA regulation or genomic locus of senseless transcription produced distinct noise signatures. Genomic location altered protein stochasticity in an allelic-pairing dependent manner (transvection). This generated sensory pattern disorder without perturbing protein abundance. In contrast, loss of microRNA repression of senseless increased protein abundance but not sensory pattern disorder. This suggests that gene expression stochasticity is a critical feature that must be constrained during development to allow rapid yet accurate cell fate resolution.One Sentence SummaryLife on the Margin: balancing speed and accuracy during animal development.

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