Combined Relaxation Spectra for the Prediction of Meat Quality: A Case Study on Broiler Breast Fillets with the Wooden Breast Condition.

This study evaluated the potential of using combined relaxation (CRelax) spectra within time-domain nuclear magnetic resonance (TD-NMR) measurements to predict meat quality. Broiler fillets affected by different severities of the wooden breast (WB) conditions were used as case-study samples because of the broader ranges of meat-quality variations. Partial least squares regression (PLSR) models were established to predict water-holding capacity (WHC) and meat texture, demonstrating superior CRelax capabilities for predicting meat quality. Additionally, a partial least squares discriminant analysis (PLS-DA) model was developed to predict WB severity based on CRelax spectra. The models exhibited high accuracy in distinguishing normal fillets from those affected by the WB condition and demonstrated competitive performance in classifying WB severity. This research contributes innovative insights into advanced spectroscopic techniques for comprehensive meat-quality evaluation, with implications for enhancing precision in meat applications.

Research Note: Relationships between texture and water property measurements in raw intact broiler breast fillets with the wooden breast condition.

Relationships between texture measurements and meat water properties were investigated in raw intact broiler breast fillets with the wooden breast (WB) condition. Texture measurements included subjective WB scores and blunt Meullenet-Owens Razor Shear (BMORS). Water properties were determined with low-field nuclear magnetic resonance (LF-NMR). Spearman correlation was used to estimate relationships between WB scores and water properties, while Pearson correlation was used for relationships between BMORS force and water properties. LF-NMR measurements exhibited 3 water components: protein-associated or hydration water T2b, intra-myofibrillar water or immobilized water T21, and extra-myofibrillar water or free water T22 in chicken breast meat. Significant and strong Spearman correlations were found between the WB scores and T21 time constant, the abundance (normalized areas) of T22, and the proportion of T21 and T22 (rs > 0.60, P < 0.001). Strong Pearson correlations (r = 0.72) were noted only between the T21 time constant and BMORS force. These results demonstrate that water may contribute to the specific texture characteristics measured with subjective WB scoring (palpable hardness and rigidity) and BMORS (hardness and share force) in raw broiler breast fillets with the WB condition.

Fine-tuning activation specificity of G-protein-coupled receptors via automated path searching.

Physics-based simulation methods can grant atomistic insights into the molecular origin of the function of biomolecules. However, the potential of such approaches has been hindered by their low efficiency, including in the design of selective agonists where simulations of myriad protein-ligand combinations are necessary. Here, we describe an automated input-free path searching protocol that offers (within 14 d using Graphics Processing Unit servers) a minimum free energy path (MFEP) defined in high-dimension configurational space for activating sphingosine-1-phosphate receptors (S1PRs) by arbitrary ligands. The free energy distributions along the MFEP for four distinct ligands and three S1PRs reached a remarkable agreement with Bioluminescence Resonance Energy Transfer (BRET) measurements of G-protein dissociation. In particular, the revealed transition state structures pointed out toward two S1PR3 residues F263/I284, that dictate the preference of existing agonists CBP307 and BAF312 on S1PR1/5. Swapping these residues between S1PR1 and S1PR3 reversed their response to the two agonists in BRET assays. These results inspired us to design improved agonists with both strong polar head and bulky hydrophobic tail for higher selectivity on S1PR1. Through merely three in silico iterations, our tool predicted a unique compound scaffold. BRET assays confirmed that both chiral forms activate S1PR1 at nanomolar concentration, 1 to 2 orders of magnitude less than those for S1PR3/5. Collectively, these results signify the promise of our approach in fine agonist design for G-protein-coupled receptors.

Structural insights into the activation and inhibition of CXC chemokine receptor 3.

The chemotaxis of CD4+ type 1 helper cells and CD8+ cytotoxic lymphocytes, guided by interferon-inducible CXC chemokine 9-11 (CXCL9-11) and CXC chemokine receptor 3 (CXCR3), plays a critical role in type 1 immunity. Here we determined the structures of human CXCR3-DNGi complexes activated by chemokine CXCL11, peptidomimetic agonist PS372424 and biaryl-type agonist VUF11222, and the structure of inactive CXCR3 bound to noncompetitive antagonist SCH546738. Structural analysis revealed that PS372424 shares a similar orthosteric binding pocket to the N terminus of CXCL11, while VUF11222 buries deeper and activates the receptor in a distinct manner. We showed an allosteric binding site between TM5 and TM6, accommodating SCH546738 in the inactive CXCR3. SCH546738 may restrain the receptor at an inactive state by preventing the repacking of TM5 and TM6. By revealing the binding patterns and the pharmacological properties of the four modulators, we present the activation mechanisms of CXCR3 and provide insights for future drug development.

Mechanism of agonist-induced activation of the human itch receptor MRGPRX1.

Mas-related G-protein-coupled receptors X1-X4 (MRGPRX1-X4) are 4 primate-specific receptors that are recently reported to be responsible for many biological processes, including itch sensation, pain transmission, and inflammatory reactions. MRGPRX1 is the first identified human MRGPR, and its expression is restricted to primary sensory neurons. Due to its dual roles in itch and pain signaling pathways, MRGPRX1 has been regarded as a promising target for itch remission and pain inhibition. Here, we reported a cryo-electron microscopy (cryo-EM) structure of Gq-coupled MRGPRX1 in complex with a synthetic agonist compound 16 in an active conformation at an overall resolution of 3.0 Å via a NanoBiT tethering strategy. Compound 16 is a new pain-relieving compound with high potency and selectivity to MRGPRX1 over other MRGPRXs and opioid receptor. MRGPRX1 was revealed to share common structural features of the Gq-mediated receptor activation mechanism of MRGPRX family members, but the variable residues in orthosteric pocket of MRGPRX1 exhibit the unique agonist recognition pattern, potentially facilitating to design MRGPRX1-specific modulators. Together with receptor activation and itch behavior evaluation assays, our study provides a structural snapshot to modify therapeutic molecules for itch relieving and analgesia targeting MRGPRX1.

An LC-MS-based workflow measures the export activity of S1P transporters.

Sphingosine-1-phosphate (S1P) is an active signaling metabolite synthesized by blood cells, exported into blood stream, and can trigger many downstream signaling pathways with disease implications. Understanding how S1P is transported is of great values for dissecting the function of S1P, but most existing methods for measuring S1P transporter activity use radioactive substrates or involve multiple workup steps, hindering their broader uses. In this study, we develop a workflow combining sensitive LC-MS measurement and a cell-based transporter protein system to measure the export activity of S1P transporter proteins. Our workflow demonstrated good applications in studying different S1P transporters SPNS2 and MFSD2B, WT and mutated protein, and different protein substrates. In summary, we provide a simple yet versatile workflow for measuring the export activity of S1P transporters, facilitating future studies of S1P transport mechanism and drug development.

A high-throughput KASP assay provides insights into the evolution of multiple resistant mutations in populations of the two-spotted spider mite Tetranychus urticae across China.

BACKGROUND: The two-spotted spider mite (TSSM), Tetranychus urticae (Acari: Tetranychidae), is a cosmopolitan phytophagous pest in agriculture and horticulture. It has developed resistance to many acaricides by target-site mutations. Understanding the status and evolution of resistant mutations in the field is essential for resistance management. Here, we applied a high-throughput Kompetitive allele-specific polymerase chain reaction (KASP) method for detecting six mutations conferring resistance to four acaricides of the TSSM. We genotyped 3274 female adults of TSSM from 43 populations collected across China in 2017, 2020, and 2021. RESULTS: The KASP genotyping of 24 testing individuals showed 99% agreement with Sanger sequencing results. KASP assays showed that most populations had a high frequency of mutations conferring avermectin (G314D and G326E) and pyridaben (H92R) resistance. The frequency of mutation conferring bifenazate (A269V and G126S) and etoxazole (I1017F) resistance was relatively low. Multiple mutations were common in the TSSM, with 70.2% and 24.6% of individuals having 2-6 and 7-10 of 10 possible resistant alleles, respectively. No loci were linked in most populations among the six mutations, indicating the development of multiple resistance is mainly by independent selection. However, G314D and I1017F on the nuclear genome deviated from Hardy-Weinberg equilibrium in most populations, indicating significant selective pressure on TSSM populations by acaricides or fitness cost of the mutations in the absence of acaricide selection. CONCLUSION: Our study revealed that the high frequency of TSSMs evolved multiple resistant mutations in population and individual levels by independent selection across China, alarming for managing multiple-acaricides resistance. © 2023 Society of Chemical Industry.

KASP genotyping and semi-quantitation of G275E mutation in the α6 subunit of Thrips palmi nAChR gene conferring spinetoram resistance.

BACKGROUND: Pesticide resistance is a long-standing and growing problem in the chemical control of invertebrate pests. Molecular diagnostic methods can facilitate pesticide resistance management by accurately and efficiently detecting resistant mutations and their frequency. In this study, the kompetitive allele specific PCR (KASP) approach, a technology for high-throughput single nucleotide polymorphism (SNP) genotyping, is validated as a useful method for characterizing genotypes at a pesticide-resistance locus for the first time. We focus on the spinetoram resistance mutation of G275E in the nicotinic acetylcholine receptor alpha 6 (nAChR α6) subunit gene of Thrips palmi. RESULTS: Of the 341 individuals of Thrips palmi tested, 98.24% were successfully genotyped, with 100% concordance with Sanger sequencing results. We then quantitatively mixed genomic DNA of known genotypes to establish 21 DNA mixtures with a resistant allele frequency ranging from 0 to 100% at steps of 5%. The linear discriminant analysis (LDA) showed that 75.8% of original grouped cases were correctly classified; six groups had no overlap in membership (resistant allele frequency: 0%, 5%, 10-75%, 80-85%, 90-95%, and 100%). When we chose 11 pooled samples with 10% steps for LDA, 84.4% of original grouped cases were correctly classified; seven groups had no overlap in membership (0%, 10%, 20-30%, 40-70%, 80%, 90%, 100%). The results indicated that KASP applied to pooled samples may provide a semi-quantitative estimate of resistance. CONCLUSIONS: Our study points to the suitability of KASP for high-throughput genotyping of genotypes affecting pesticide resistance and semi-quantitative assessments of resistance allele frequencies in populations. © 2023 Society of Chemical Industry.

Integration of multi-omics data reveals cis-regulatory variants that are associated with phenotypic differentiation of eastern from western pigs.

BACKGROUND: The genetic mechanisms that underlie phenotypic differentiation in breeding animals have important implications in evolutionary biology and agriculture. However, the contribution of cis-regulatory variants to pig phenotypes is poorly understood. Therefore, our aim was to elucidate the molecular mechanisms by which non-coding variants cause phenotypic differences in pigs by combining evolutionary biology analyses and functional genomics. RESULTS: We obtained a high-resolution phased chromosome-scale reference genome with a contig N50 of 18.03 Mb for the Luchuan pig breed (a representative eastern breed) and profiled potential selective sweeps in eastern and western pigs by resequencing the genomes of 234 pigs. Multi-tissue transcriptome and chromatin accessibility analyses of these regions suggest that tissue-specific selection pressure is mediated by promoters and distal cis-regulatory elements. Promoter variants that are associated with increased expression of the lysozyme (LYZ) gene in the small intestine might enhance the immunity of the gastrointestinal tract and roughage tolerance in pigs. In skeletal muscle, an enhancer-modulating single-nucleotide polymorphism that is associated with up-regulation of the expression of the troponin C1, slow skeletal and cardiac type (TNNC1) gene might increase the proportion of slow muscle fibers and affect meat quality. CONCLUSIONS: Our work sheds light on the molecular mechanisms by which non-coding variants shape phenotypic differences in pigs and provides valuable resources and novel perspectives to dissect the role of gene regulatory evolution in animal domestication and breeding.

Bearing Fault Diagnosis Based on an Enhanced Image Representation Method of Vibration Signal and Conditional Super Token Transformer.

Multipoint Optimal Minimum Entropy Deconvolution Adjusted (MOMEDA) is an advanced deconvolution method, which can effectively inhibit the interference of background noise and distinguish the fault period by calculating the multipoint kurtosis values. However, multipoint kurtosis (MKurt) could lead to misjudgment since it is sensitive to spurious noise spikes. Considering that L-kurtosis has good robustness with noise, this paper proposes a multipoint envelope L-kurtosis (MELkurt) method for establishing the temporal features. Then, an enhanced image representation method of vibration signals is proposed by employing the Gramian Angular Difference Field (GADF) method to convert the MELkurt series into images. Furthermore, to effectively learn and extract the features of GADF images, this paper develops a deep learning method named Conditional Super Token Transformer (CSTT) by incorporating the Super Token Transformer block, Super Token Mixer module, and Conditional Positional Encoding mechanism into Vision Transformer appropriately. Transfer learning is introduced to enhance the diagnostic accuracy and generalization capability of the designed CSTT. Consequently, a novel bearing fault diagnosis framework is established based on the presented enhanced image representation and CSTT. The proposed method is compared with Vision Transformer and some CNN-based models to verify the recognition effect by two experimental datasets. The results show that MELkurt significantly improves the fault feature enhancement ability with superior noise robustness to kurtosis, and the proposed CSTT achieves the highest diagnostic accuracy and stability.

Synergistic effect of preheating and different power output high-intensity ultrasound on the physicochemical, structural, and gelling properties of myofibrillar protein from chicken wooden breast.

The effects of preheating to 50 ℃ and the subsequent application of high-intensity ultrasound (HIU, 20 kHz) at 200, 400, 600, and 800 W on the physicochemical, structural, and gelling properties of wooden breast myofibrillar protein (WBMP) were studied. Results suggested that the WBMP structure expanded to the balanced state at 600 W, and rheological properties exhibit that 600 W HIU (P < 0.05) significantly improved the storage modulus (G') of WBMP. Notably, the WBMP gel (600 W) had the best hardness (65.428 ± 0.33 g), springiness (0.582 ± 0.01), and water-holding capacity (86.11 ± 0.83%). Raman spectra and low-field NMR indicated that 600 W HIU increased the ß-fold content (37.94 ± 0.04%) and enlarged the immobilized-water proportion (93.87 ± 0.46%). Scanning electron micrographs confirmed that the gel was uniform and dense at 600 W. Therefore, preheating to 50 ℃ followed by HIU (600 W) helped form a superior WBMP gel.

Water properties and marinade uptake in broiler pectoralis major with the woody breast condition.

To provide insight into the mechanisms by which the woody breast (WB) condition reduces marinade uptake, water properties of normal (NOR) and WB meat were investigated using TD-NMR. Broiler Pectoralis major was marinated with either water, 0.625% sodium tripolyphosphate, 5% NaCl, or 5% NaCl + 0.625% sodium tripolyphosphate (SP). Targeted final concentrations were 4% NaCl and 0.5% SP. WB reduced meat marinade uptake but did not affect relationships between marinade ingredients and water mobility. WB inhibited increases in extra-myofibrillar water mobility induced by marinade ingredients. Marination increased intra-myofibrillar water (Amp21) regardless of marinade ingredients or muscle condition; however, WB resulted in reduced Amp21. Additionally, NaCl- or phosphate-induced extra-myofibrillar water (Amp22) gain in WB was greater than that in NOR. Our data suggest changes in both Amp21 and Amp22 are related to the difference in marinade uptake between NOR and WB meat marinated with NaCl-phosphate marinade.

Comparative transcriptome and DNA methylation analysis in temperature-sensitive genic male sterile wheat BS366.

BACKGROUND: Known as the prerequisite component for the heterosis breeding system, the male sterile line determines the hybrid yield and seed purity. Therefore, a deep understanding of the mechanism and gene network that leads to male sterility is crucial. BS366, a temperature-sensitive genic male sterile (TGMS) line, is male sterile under cold conditions (12 °C with 12 h of daylight) but fertile under normal temperature (20 °C with 12 h of daylight). RESULTS: During meiosis, BS366 was defective in forming tetrads and dyads due to the abnormal cell plate. During pollen development, unusual vacuolated pollen that could not accumulate starch grains at the binucleate stage was also observed. Transcriptome analysis revealed that genes involved in the meiotic process, such as sister chromatid segregation and microtubule-based movement, were repressed, while genes involved in DNA and histone methylation were induced in BS366 under cold conditions. MethylRAD was used for reduced DNA methylation sequencing of BS366 spikes under both cold and control conditions. The differentially methylated sites (DMSs) located in the gene region were mainly involved in carbohydrate and fatty acid metabolism, lipid metabolism, and transport. Differentially expressed and methylated genes were mainly involved in cell division. CONCLUSIONS: These results indicated that the methylation of genes involved in carbon metabolism or fatty acid metabolism might contribute to male sterility in BS366 spikes, providing novel insight into the molecular mechanism of wheat male sterility.

Evaluation of multi blade shear (MBS) for determining texture of raw and cooked broiler breast fillets with the woody breast myopathy.

The objective of this study was to evaluate a novel multi-blade Shear (MBS) method for measuring texture properties of both raw and cooked broiler fillets (pectoralis major) with the woody breast (WB) myopathy. A total of 180 broiler breast fillets (60 normal [NOR], 60 moderate WB [MOD], and 60 severe WB [SEV]) in two meat states (fresh never-frozen, n = 144; frozen/thawed, n = 36) were chosen based on their WB scores. In each trial, half of the fillets were used for measuring raw meat texture and the other half for cooked meat texture measurement. Blunt Meullenet-Owens Razor Sear (BMORS) was used for comparison. In fresh raw broiler fillets, both the MBS and BMORS methods detected differences between NOR, MOD, and SEV fillets (P < 0.001). In cooked broiler fillets, the methods were equivalent in their ability to separate SEV from NOR fillets. The MBS measurements showed greater Spearman correlation coefficients with the WB scores (rs ≥ 0.70 in raw and ≥ 0.33 in cooked) compared to the BMORS measurements (rs = 0.63 in raw and ≤ 0.27 in cooked) for both fresh and cooked breast fillets. In addition, the MBS measurements were either as precise as or more precise than BMORS measurements regardless of meat condition (fresh vs. cooked) and the shear parameter. These results suggest that the MBS method is more reliable in measuring tactile characteristics of broiler breast fillets with the WB myopathy compared with the BMORS method.

Genome-wide identification and transcriptional characterization of DNA methyltransferases conferring temperature-sensitive male sterility in wheat.

BACKGROUND: DNA methyltransferase (DMT) genes contribute to plant stress responses and development by de novo establishment and subsequent maintenance of DNA methylation during replication. The photoperiod and/or temperature-sensitive genic male sterile (P/TGMS) lines play an important role in hybrid seed production of wheat. However, only a few studies have reported on the effect of DMT genes on temperature-sensitive male sterility of wheat. Although DMT genes have been investigated in some plant species, the identification and analysis of DMT genes in wheat (Triticum aestivum L.) based on genome-wide levels have not been reported. RESULTS: In this study, a detailed overview of phylogeny of 52 wheat DMT (TaDMT) genes was presented. Homoeolog retention for TaDMT genes was significantly above the average retention rate for whole-wheat genes, indicating the functional importance of many DMT homoeologs. We found that the strikingly high number of TaDMT genes resulted mainly from the significant expansion of the TaDRM subfamily. Intriguingly, all 5 paralogs belonged to the wheat DRM subfamily, and we speculated that tandem duplications might play a crucial role in the TaDRM subfamily expansion. Through the transcriptional analysis of TaDMT genes in a TGMS line BS366 and its hybrids with the other six fertile lines under sterile and fertile conditions, we concluded that TaCMT-D2, TaMET1-B1, and TaDRM-U6 might be involved in male sterility in BS366. Furthermore, a correlation analysis showed that TaMET1-B1 might negatively regulate the expression of TaRAFTIN1A, an important gene for pollen development, so we speculated regarding an epigenetic regulatory mechanism underlying the male sterility of BS366 via the interaction between TaMET1-B1 and TaRAFTIN1A. CONCLUSIONS: Our findings presented a detailed phylogenic overview of the DMT genes and could provide novel insights into the effects of DMT genes on TGMS wheat.

Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism.

Steroid hormones are essential in stress response, immune system regulation, and reproduction in mammals. Steroids with 3-oxo-Δ4 structure, such as testosterone or progesterone, are catalyzed by steroid 5α-reductases (SRD5As) to generate their corresponding 3-oxo-5α steroids, which are essential for multiple physiological and pathological processes. SRD5A2 is already a target of clinically relevant drugs. However, the detailed mechanism of SRD5A-mediated reduction remains elusive. Here we report the crystal structure of PbSRD5A from Proteobacteria bacterium, a homolog of both SRD5A1 and SRD5A2, in complex with the cofactor NADPH at 2.0 Å resolution. PbSRD5A exists as a monomer comprised of seven transmembrane segments (TMs). The TM1-4 enclose a hydrophobic substrate binding cavity, whereas TM5-7 coordinate cofactor NADPH through extensive hydrogen bonds network. Homology-based structural models of HsSRD5A1 and -2, together with biochemical characterization, define the substrate binding pocket of SRD5As, explain the properties of disease-related mutants and provide an important framework for further understanding of the mechanism of NADPH mediated steroids 3-oxo-Δ4 reduction. Based on these analyses, the design of therapeutic molecules targeting SRD5As with improved specificity and therapeutic efficacy would be possible.

A Glimpse of the Structural Biology of the Metabolism of Sphingosine-1-Phosphate.

As a key sphingolipid metabolite, sphingosine-1-phosphate (S1P) plays crucial roles in vascular and immune systems. It regulates angiogenesis, vascular integrity and homeostasis, allergic responses, and lymphocyte trafficking. S1P is interconverted with sphingosine, which is also derived from the deacylation of ceramide. S1P levels and the ratio to ceramide in cells are tightly regulated by its metabolic pathways. Abnormal S1P production causes the occurrence and progression of numerous severe diseases, such as metabolic syndrome, cancers, autoimmune disorders such as multiple sclerosis, and kidney and cardiovascular diseases. In recent years, huge advances on the structure of S1P metabolic pathways have been accomplished. In this review, we have got a glimpse of S1P metabolism through structural and biochemical studies of: sphingosine kinases, S1P transporters and S1P receptors, and the development of therapeutics targeting S1P signaling. The progress we summarize here could provide fresh perspectives to further the exploration of S1P functions and facilitate the development of therapeutic molecules targeting S1P signaling with improved specificity and therapeutic effects.