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Abstract Background Heritability partitioning approaches estimate the contribution of different functional classes, such as coding or regulatory variants, to the genetic variance. This information allows a better understanding of the genetic architecture of complex traits, including complex diseases, but can also help improve the accuracy of genomic selection in livestock species. However, methods have mainly been tested on human genomic data, whereas livestock populations have specific characteristics, such as high levels of relatedness, small effective population size or long-range levels of linkage disequilibrium. Results Here, we used data from 14,762 cows, imputed at the whole-genome sequence level for 11,537,240 variants, to simulate traits in a typical livestock population and evaluate the accuracy of two state-of-the-art heritability partitioning methods, GREML and a Bayesian mixture model. In simulations where a single functional class had increased contribution to heritability, we observed that the estimators were unbiased but had low precision. When causal variants were enriched in variants with low ( 0.20) minor allele frequency or low (below 1st quartile) or high (above 3rd quartile) linkage disequilibrium scores, it was necessary to partition the genetic variance into multiple classes defined on the basis of allele frequencies or LD scores to obtain unbiased results. When multiple functional classes had variable contributions to heritability, estimators showed higher levels of variation and confounding between certain categories was observed. In addition, estimators from small categories were particularly imprecise. However, the estimates and their ranking were still informative about the contribution of the classes. We also demonstrated that using methods that estimate the contribution of a single category at a time, a commonly used approach, results in an overestimation. Finally, we applied the methods to phenotypes for muscular development and height and estimated that, on average, variants in open chromatin regions had a higher contribution to the genetic variance (> 45%), while variants in coding regions had the strongest individual effects (> 25-fold enrichment on average). Conversely, variants in intergenic or intronic regions showed lower levels of enrichment (0.2 and 0.6-fold on average, respectively). Conclusions Heritability partitioning approaches should be used cautiously in livestock populations, in particular for small categories. Two-component approaches that fit only one functional category at a time lead to biased estimators and should not be used.

The objective of this study was to assess and compare the characteristics of Yu-Shiang Shredded Pork made with different ingredients by using physicochemical measurements and intelligent sensory analysis. The study revealed that there were 18 varied amino acids present, with the taste active values (TAVs) of Leu, Glu, Asp, Asn, and Ala all higher than 1.0. Intelligent sensory analysis showed that the samples lacking lettuce and fungus had similar aromas and flavors, while those lacking shredded pork and pickled chillies had distinct aromas and flavors. Moreover, VOCs (volatile organic compounds) were detected in five types of Yu-Shiang Shredded Pork, with 43, 42, 53, 36, and 50 identified in GC-MS (gas chromatography-mass spectrometry), respectively. Olefins (20.62 %–30.93 %) were the most abundant. GC-IMS (gas chromatography-ion mobility spectrometry) detected 68 volatiles flavor compounds, with esters having a significantly higher relative content than other compounds, indicating their significant role in the flavor formation process of Yu-Shiang Shredded Pork. Furthermore, the Orthogonal Partial Least Squares-discriminant analysis (OPLS-DA) model analysis identified 19 marker compounds that could differentiate the five types of Yu-Shiang Shredded Pork. These fundamental results lay the groundwork for future research on the connection between ingredients and the flavor characteristics of Yu-Shiang Shredded Pork.

Abstract Background Cohorts of individuals that have been genotyped and phenotyped for genomic selection programs offer the opportunity to better understand genetic variation associated with complex traits. Here, we performed an association study for traits related to body size and muscular development in intensively selected beef cattle. We leveraged multiple trait information to refine and interpret the significant associations. Results After a multiple-step genotype imputation to the sequence-level for 14,762 Belgian Blue beef (BBB) cows, we performed a genome-wide association study (GWAS) for 11 traits related to muscular development and body size. The 37 identified genome-wide significant quantitative trait loci (QTL) could be condensed in 11 unique QTL regions based on their position. Evidence for pleiotropic effects was found in most of these regions (e.g., correlated association signals, overlap between credible sets (CS) of candidate variants). Thus, we applied a multiple-trait approach to combine information from different traits to refine the CS. In several QTL regions, we identified strong candidate genes known to be related to growth and height in other species such as LCORL-NCAPG or CCND2. For some of these genes, relevant candidate variants were identified in the CS, including three new missense variants in EZH2, PAPPA2 and ADAM12, possibly two additional coding variants in LCORL, and candidate regulatory variants linked to CCND2 and ARMC12. Strikingly, four other QTL regions associated with dimension or muscular development traits were related to five (recessive) deleterious coding variants previously identified. Conclusions Our study further supports that a set of common genes controls body size across mammalian species. In particular, we added new genes to the list of those associated with height in both humans and cattle. We also identified new strong candidate causal variants in some of these genes, strengthening the evidence of their causality. Several breed-specific recessive deleterious variants were identified in our QTL regions, probably as a result of the extreme selection for muscular development in BBB cattle.

To understand the effects of particle size on the extraction of volatile huajiao (HJ) Zanthoxylum oils, Hanyuan pepper powder of 20, 30, 40, 60, and 80 mesh sizes was fried at 130 ℃ for 20 minutes with rapeseed oil as the extract oil. E-nose, gas chromatography-ion mobility spectrometry (GC-IMS), gas chromatography-mass spectrometer (GC-MS), odor activity value (OAV), and quantitative descriptive analysis (QDA) were applied to analyze the volatile Zanthoxylum oil components extracted from different sizes of pepper particles. Cluster analysis and Pearson correlation were performed to explore the differences in aroma profiles between samples. The E-nose and CA results indicated that the HJ-1 (20 mesh) sample was clearly different from other samples in terms of aroma, the aroma characteristics of HJ-4 (60 mesh) and HJ-5 (80 mesh) samples were similar, and the aroma characteristics of HJ-2 (30 mesh) and HJ-3 (40 mesh) samples were similar to each other. A total of 118 aromatic components were detected by GC-IMS, comprising 20 unidentified components and 98 identified components. The identified compounds included 13 aldehydes, 11 ketones, 12 alcohols, 22 esters, 16 heterocycles, seven acid, two phenolic compounds, and eight miscellaneous components. Moreover, the OAV values of 14 key aromatic components were greater than 1, including linalool, 2-furanmethanol, 2-phenylethanol, linalyl acetate, methyl phenyl acetate, γ-terpinene, phellandrene, and β-pinene. The key aromatic components of the HJ-4 sample contributed the most to the aroma of Zanthoxylum oil. QDA analysis revealed that the HJ-4 samples had very strong woody, lemon, nutty and fatty flavors. The Pearson correlation coefficient showed that the sensory property of lemon, woody, nutty and fatty flavors and concentrations of most key aromatic were strongly and positively correlated. From comprehensive analysis, the HJ-4 sample prepared from 60 mesh pepper powder was determined to have the best aroma sensory quality. In conclusion, GC-IMS and OAV values were able to identify the effect of different sizes of pepper particles during the extraction of volatile components of Zanthoxylum oil. This information could be used to provide a theoretical and practical reference for the production of Zanthoxylum oil.

A single combi oven, known for its versatility, is an excellent choice for a variety of chicken soup preparations. However, the impact of universal steam ovens on the flavor quality of chicken soup remains unclear. This study aimed to explore the impact of different cooking methods on the aroma and taste of chicken soup. Three cooking methods with various stewing times were compared: ceramic pot (CP), electric pressure cooker (EPC), and combi oven (CO). Analyses were conducted using electron-nose, electron-tongue, gas chromatography–ion mobility spectrometry (GC–IMS), automatic amino acid analysis, and chemometric methods. A total of 14 amino acids, including significant umami contributors, were identified. The taste components of CP and CO chicken soups were relatively similar. In total, 39 volatile aroma compounds, predominantly aldehydes, ketones, and alcohols, were identified. Aldehydes were the most abundant compounds, and 23 key aroma compounds were identified. Pearson’s correlation analyses revealed distinct correlations between various amino acids (e.g., glutamic acid and serine) and specific volatile compounds. The aroma compounds from the CP and CO samples showed similarities. The results of this study provide a reference for the application of one-touch cooking of chicken soup in versatile steam ovens.

In order to identify the overall flavor information of Yu-shiang Shredded Pork Seasoning quickly and accurately, the difference of the smell and taste analysis for different brands Yu-shiang Shredded Pork Seasoning were evaluated by electronic nose and electronic tongue，combined with automatic amino acid analyzer to study the relationship between the free amino acid and E-tongue taste property. This study indicated that the electronic nose could distinguish the different brands of Yu-shiang Shredded Pork Seasoning accurately. The aroma between B and C samples was relatively similar. Moreover, there were significant differences among the aroma of other samples. Electronic tongue could be better to distinguish the taste of various samples. The sour taste of D sample was outstanding, the sweet taste of A sample was highlighted, the salty and umami taste of E sample were prominent. The taste active value of glutamic acid, alanine, valine, phenylalanine and histidine in sample E was higher than 1.0, indicating that it had a great contribution to the umami and sweet taste of Yu-shiang Shredded Pork Seasoning. The analysis of partial least squae and Pearson correlations showed that the E-tongue taste property was positively associated with most free amino acid. The sour and sweet taste were significantly correlated with the concentrations of threonine and glycine respectively (P

Abstract Ligusticum L., one of the largest members in Apiaceae, encompasses medicinally important plants, the taxonomic statuses of which have been proved to be difficult to resolve. In the current study, the complete chloroplast genomes of seven crucial plants of the best-known herbs in Ligusticum were presented. The seven genomes ranged from 148,275 to 148,564 bp in length with a highly conserved gene content, gene order and genomic arrangement. A shared dramatic decrease in genome size resulted from a lineage-specific inverted repeat (IR) contraction, which could potentially be a promising diagnostic character for taxonomic investigation of Ligusticum, was discovered, without affecting the synonymous rate. Although a higher variability was uncovered in hotspot divergence regions that were unevenly distributed across the chloroplast genome, a concatenated strategy for rapid species identification was proposed because separate fragments inadequately provided variation for fine resolution. Phylogenetic inference using plastid genome-scale data produced a concordant topology receiving a robust support value, which revealed that L. chuanxiong had a closer relationship with L. jeholense than L. sinense, and L. sinense cv. Fuxiong had a closer relationship to L. sinense than L. chuanxiong, for the first time. Our results not only furnish concrete evidence for clarifying Ligusticum taxonomy but also provide a solid foundation for further pharmaphylogenetic investigation.

The hot deformation behavior of Mg-6Gd-5Y-0.3Zr alloy at the temperatures of 673–748 K and the strain rates of 0.01–1.0 s−1 were investigated by hot compression experiments. On this basis, a physically based internal state variable (ISV) model coupling the microstructural evolution was established, in which the ISVs of the model included dislocation density, grain size and volume fraction of dynamic recrystallization (DRX). Besides, the recrystallized and un-recrystallized grain sizes were considered to characterize the evolution process of microstructure. By comparing the calculated and experimental flow stresses, the model was proved to be reliable. Then the model was imported into the finite element analysis (FEA) software ABAQUS to predict the ISV evolution of Mg-6Gd-5Y-0.3Zr alloy in the hot extrusion process. The comparative analysis of the simulation and experimental results further verified the applicability of the constitutive model established in this study.

Leaves start to develop at the peripheral zone of the shoot apical meristem. Thereafter, symmetric and flattened leaf laminae are formed. These events are simultaneously regulated by auxin, transcription factors, and epigenetic regulatory factors. However, the relationships among these factors are not well known. In this study, we conducted protein-protein interaction assays to show that our previously reported Leaf and Flower Related (LFR) physically interacted with SWI3B, a component of the ATP-dependent chromatin remodeling SWI/SNF complex in Arabidopsis. The results of truncated analysis and transgenic complementation showed that the N-terminal domain (25–60 amino acids) of LFR was necessary for its interaction with SWI3B and was crucial for LFR functions in Arabidopsis leaf development. Genetic results showed that the artificial microRNA knockdown lines of SWI3B (SWI3B-amic) had a similar upward-curling leaf phenotype with that of LFR loss-of-function mutants. ChIP-qPCR assay was conducted to show that LFR and SWI3B co-targeted the promoters of YABBY1/FILAMENTOUS FLOWER (YAB1/FIL) and IAA carboxyl methyltransferase 1 (IAMT1), which were misexpressed in lfr and SWI3B-amic mutants. In addition, the association between LFR and the FIL and IAMT1 loci was partly hampered by the knockdown of SWI3B. These data suggest that LFR interacts with the chromatin-remodeling complex component, SWI3B, and influences the transcriptional expression of the important transcription factor, FIL, and the auxin metabolism enzyme, IAMT1, in flattened leaf lamina development.

The prestress loss is one of the main factors affecting the safety of prestressed concrete structure. While the detecting signals like sound and light are difficult to spread in steel strands, there is no effective method for prestress detection of the bonded prestressed steel strands in existing structures yet. In this paper, taking into consideration that the electromagnetic oscillation characteristic can make the signal propagate effectively on the bonded prestressed steel strands, a nondestructive prestress detection method based on the electromagnetic effect to detect oscillation frequency is proposed. In a detection circuit, the steel strands are simulated as an inductance component, in which an induced electromagnetic signal passes through the steel strands to form resonance. And then, a frequency meter is used to detect the oscillation frequency of the resonant circuit. The oscillation frequency is supposed to have relationship with the prestress loading on the steel strands. A section of steel strands with a length of 1.2 m is adopted to test the correlation of stress and oscillation frequency. Both the theoretical and experimental results show that the resonant frequency of the circuit decreases with the increase of the stress of the strand and is linear in a certain range.

Ophiopogon japonicus, extensively distributed in East Asia, is widely used in landscaping, the tuber of which also play a vital role in Oriental Medicine. Here, we reported the complete chloroplast genome which exhibited a typical quadripartite structure, 156,679 bp in length with 37.7% overall GC content, including 131 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes, and one pseudogene. Phylogenetic analysis suggested that O. japonicus has a close relationship to Liriope spicata.

Previous studies have shown that multivesicular bodies (MVBs)/endosomes-mediated vesicular trafficking may play key roles in plant immunity and cell death. However, the molecular regulation is poorly understood in rice. Here we report the identification and characterization of a MVBs-localized AAA ATPase LRD6-6 in rice. Disruption of LRD6-6 leads to enhanced immunity and cell death in rice. The ATPase activity and homo-dimerization of LRD6-6 is essential for its regulation on plant immunity and cell death. An ATPase inactive mutation (LRD6-6E315Q) leads to dominant-negative inhibition in plants. The LRD6-6 protein co-localizes with the MVBs marker protein RabF1/ARA6 and interacts with ESCRT-III components OsSNF7 and OsVPS2. Further analysis reveals that LRD6-6 is required for MVBs-mediated vesicular trafficking and inhibits the biosynthesis of antimicrobial compounds. Collectively, our study shows that the AAA ATPase LRD6-6 inhibits plant immunity and cell death most likely through modulating MVBs-mediated vesicular trafficking in rice.

CaV1.3 channels regulate excitability in many neurons. As is the case for all voltage-gated channels, it is widely assumed that individual CaV1.3 channels behave independently with respect to voltage-activation, open probability, and facilitation. Here, we report the results of super-resolution imaging, optogenetic, and electrophysiological measurements that refute this long-held view. We found that the short channel isoform (CaV1.3S), but not the long (CaV1.3L), associates in functional clusters of two or more channels that open cooperatively, facilitating Ca2+ influx. CaV1.3S channels are coupled via a C-terminus-to-C-terminus interaction that requires binding of the incoming Ca2+ to calmodulin (CaM) and subsequent binding of CaM to the pre-IQ domain of the channels. Physically-coupled channels facilitate Ca2+ currents as a consequence of their higher open probabilities, leading to increased firing rates in rat hippocampal neurons. We propose that cooperative gating of CaV1.3S channels represents a mechanism for the regulation of Ca2+ signaling and electrical activity.

Panax notoginseng is famous for its important therapeutic effects and commonly used worldwide. The active ingredients saponins have distinct contents in different tissues of P. notoginseng, and they may be related to the expression of key genes in the synthesis pathway. In our study, high-performance liquid chromatography results indicated that the contents of protopanaxadiol-(Rb1, Rc, Rb2, and Rd) and protopanaxatriol-type (R1, Rg1, and Re) saponins in below ground tissues were higher than those in above ground tissues. Clustering dendrogram and PCA analysis suggested that the below and above ground tissues were clustered into two separate groups. A total of 482 and 882 unigenes were shared in the below and above ground tissues, respectively. A total of 75 distinct expressions of CYPs transcripts (RPKM ≥ 10) were detected. Of these transcripts, 38 and 37 were highly expressed in the below ground and above ground tissues, respectively. RT-qPCR analysis showed that CYP716A47 gene was abundantly expressed in the above ground tissues, especially in the flower, whose expression was 31.5-fold higher than that in the root. CYP716A53v2 gene was predominantly expressed in the below ground tissues, especially in the rhizome, whose expression was 20.1-fold higher than that in the flower. Pearson’s analysis revealed that the CYP716A47 expression was significantly correlated with the contents of ginsenoside Rc and Rb2. The CYP716A53v2 expression was associated with the saponin contents of protopanaxadiol-type (Rb1 and Rd) and protopanaxatriol-type (R1, Rg1, and Re). Results indicated that the expression patterns of CYP716A47 and CYP716A53v2 were correlated with the distribution of protopanaxadiol-type and protopanaxatriol-type saponins in P. notoginseng. This study identified the pivotal genes regulating saponin distribution and provided valuable information for further research on the mechanisms of saponin synthesis, transportation, and accumulation.

In the heart, reliable activation of Ca2+ release from the sarcoplasmic reticulum during the plateau of the ventricular action potential requires synchronous opening of multiple CaV1.2 channels. Yet the mechanisms that coordinate this simultaneous opening during every heartbeat are unclear. Here, we demonstrate that CaV1.2 channels form clusters that undergo dynamic, reciprocal, allosteric interactions. This ‘functional coupling’ facilitates Ca2+ influx by increasing activation of adjoined channels and occurs through C-terminal-to-C-terminal interactions. These interactions are initiated by binding of incoming Ca2+ to calmodulin (CaM) and proceed through Ca2+/CaM binding to the CaV1.2 pre-IQ domain. Coupling fades as [Ca2+]i decreases, but persists longer than the current that evoked it, providing evidence for ‘molecular memory’. Our findings suggest a model for CaV1.2 channel gating and Ca2+-influx amplification that unifies diverse observations about Ca2+ signaling in the heart, and challenges the long-held view that voltage-gated channels open and close independently.

The growth process of Bacillus thuringiensis Bt4.0718 strain was studied using proteomic technologies. The proteins of Bt whole cells at three phases—middle vegetative, early sporulation, and late sporulation—were extracted with lysis buffer, followed with separation by 2-DE and identified by MALDI-TOF/TOF MS. Bioactive factors such as insecticidal crystal proteins (ICPs) including Cry1Ac(3), Cry2Aa, and BTRX28, immune inhibitor (InhA), and InhA precursor were identified. InhA started to express at the middle vegetative phase, suggesting its contribution to the survival of Bt in the host body. At the early sporulation phase, ICPs started their expression. CotJC, OppA, ORF1, and SpoIVA related to the formation of crystals and spores were identified, the expression characteristics of which ensured the stable formation of crystals and spores. This study provides an important foundation for further exploration of the stable expression of ICPs, the smooth formation of crystals, and the construction of recombinant strains.

Background: Recently, chronic kidney disease (CKD)-mineral and bone disorder (MBD) has become one of common complications occurring in CKD patients. Therefore, development of a new treatment for CKD-MBD is very important in the clinic. In China, Fucoidan (FPS), a natural compound of Laminaria japonica has been frequently used to improve renal dysfunction in CKD. However, it remains elusive whether FPS can ameliorate CKD-MBD. FGF23-Klotho signaling axis is reported to be useful for regulating mineral and bone metabolic disorder in CKD-MBD. This study thereby aimed to clarify therapeutic effects of FPS in the CKD-MBD model rats and its underlying mechanisms in vivo and in vitro, compared to Calcitriol (CTR). Methods: All male rats were divided into four groups: Sham, CKD-MBD, FPS and CTR. The CKD-MBD rat models were induced by adenine administration and uninephrectomy, and received either FPS or CTR or vehicle after induction of renal injury for 21 days. The changes in parameters related to renal dysfunction and renal tubulointerstitial damage, calcium-phosphorus metabolic disorder and bone lesion were analyzed, respectively. Furthermore, at sacrifice, the kidneys and bone were isolated for histomorphometry, immunohistochemistry and Western blot. In vitro, the murine NRK-52E cells were used to investigate regulative actions of FPS or CTR on FGF23-Klotho signaling axis, ERK1/2-SGK1-NHERF-1-NaPi-2a pathway and Klotho deficiency. Results: Using the modified CKD-MBD rat model and the cultured NRK-52E cells, we indicated that FPS and CTR alleviated renal dysfunction and renal tubulointerstitial damage, improved calcium-phosphorus metabolic disorder and bone lesion, and regulated FGF23-Klotho signaling axis and ERK1/2-SGK1-NHERF-1-NaPi-2a pathway in the kidney. In addition, using the shRNA-Klotho plasmid-transfected cells, we also detected, FPS accurately activated ERK1/2-SGK1-NHERF-1-NaPi-2a pathway through Klotho loss reversal. Conclusion: In this study, we emphatically demonstrated that FPS, a natural anti-renal dysfunction drug, similar to CTR, improves renal injury-related calcium-phosphorus metabolic disorder and bone abnormality in the CKD-MBD model rats. More importantly, we firstly found that beneficial effects in vivo and in vitro of FPS on phosphorus reabsorption are closely associated with regulation of FGF23-Klotho signaling axis and ERK1/2-SGK1-NHERF-1-NaPi-2a pathway in the kidney. This study provided pharmacological evidences that FPS directly contributes to the treatment of CKD-MBD. [ABSTRACT FROM AUTHOR]