Horizontally acquired fungal killer protein genes affect cell development in mosses.

The moss Physcomitrium patens is crucial for studying plant development and evolution. Although the P. patens genome includes genes acquired from bacteria, fungi and viruses, the functions and evolutionary significance of these acquired genes remain largely unclear. Killer protein 4 (KP4) is a toxin secreted by the phytopathogenic fungus Ustilago maydis that inhibits the growth of sensitive target strains by blocking their calcium uptake. Here, we show that KP4 genes in mosses were acquired from fungi through at least three independent events of horizontal gene transfer. Two paralogous copies of KP4 (PpKP4-1 and PpKP4-2) exist in P. patens. Knockout mutants ppkp4-1 and ppkp4-2 showed cell death at the protonemal stage, and ppkp4-2 also exhibited defects in tip growth. We provide experimental evidence indicating that PpKP4-1/2 affects P. patens protonemal cell development by mediating cytoplasmic calcium and that KP4 genes are functionally conserved between P. patens and fungi. The present study provides additional insights into the role of horizontal gene transfer in land plant development and evolution.

Vinculin Identified as a Potential Biomarker in Hand-Arm Vibration Syndrome Based on iTRAQ and LC-MS/MS-Based Proteomic Analysis.

Local vibration can induce vascular injuries, one example is the hand-arm vibration syndrome (HAVS) caused by hand-transmitted vibration (HTV). Little is known about the molecular mechanism of HAVS-induced vascular injuries. Herein, the iTRAQ (isobaric tags for relative and absolute quantitation) followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was applied to conduct the quantitative proteomic analysis of plasma from specimens with HTV exposure or HAVS diagnosis. Overall, 726 proteins were identified in iTRAQ. 37 proteins upregulated and 43 downregulated in HAVS. Moreover, 37 upregulated and 40 downregulated when comparing severe HAVS and mild HAVS. Among them, Vinculin (VCL) was found to be downregulated in the whole process of HAVS. The concentration of vinculin was further verified by ELISA, and the results suggested that the proteomics data was reliable. Bioinformative analyses were used, and those proteins mainly engaged in specific biological processes like binding, focal adhesion, and integrins. The potential of vinculin application in HAVS diagnosis was validated by the receiver operating characteristic curve.

Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude.

Crucihimalaya himalaica, a close relative of Arabidopsis and Capsella, grows on the Qinghai-Tibet Plateau (QTP) about 4,000 m above sea level and represents an attractive model system for studying speciation and ecological adaptation in extreme environments. We assembled a draft genome sequence of 234.72 Mb encoding 27,019 genes and investigated its origin and adaptive evolutionary mechanisms. Phylogenomic analyses based on 4,586 single-copy genes revealed that C. himalaica is most closely related to Capsella (estimated divergence 8.8 to 12.2 Mya), whereas both species form a sister clade to Arabidopsis thaliana and Arabidopsis lyrata, from which they diverged between 12.7 and 17.2 Mya. LTR retrotransposons in C. himalaica proliferated shortly after the dramatic uplift and climatic change of the Himalayas from the Late Pliocene to Pleistocene. Compared with closely related species, C. himalaica showed significant contraction and pseudogenization in gene families associated with disease resistance and also significant expansion in gene families associated with ubiquitin-mediated proteolysis and DNA repair. We identified hundreds of genes involved in DNA repair, ubiquitin-mediated proteolysis, and reproductive processes with signs of positive selection. Gene families showing dramatic changes in size and genes showing signs of positive selection are likely candidates for C. himalaica's adaptation to intense radiation, low temperature, and pathogen-depauperate environments in the QTP. Loss of function at the S-locus, the reason for the transition to self-fertilization of C. himalaica, might have enabled its QTP occupation. Overall, the genome sequence of C. himalaica provides insights into the mechanisms of plant adaptation to extreme environments.

Exploring the influence of different processing conditions on DNA quality of collagen peptides and the feasibility of its raw material traceability.

In this work, we have presented a new method for species origin verification of collagen peptides based on DNA techniques. First, we investigate the changes in DNA during the preparation of collagen peptides including the total amount of collagen peptide DNA and the DNA degradation under different processing conditions. Secondly, we discussed the possibility of using polymerase chain reaction (PCR) for follow-up detection of collagen peptides. The results showed that the total amount of DNA decreased as the treatment intensity increased. The size of the cleaved fragments of DNA are mainly concentrated between 200 and 500 bp. On this basis, the combined PCR results finally determined that trace collagen peptide DNA can be effectively amplified with amplicons of about 300 bp to complete the verification of the species origin of collagen peptide. This study provides a new strategy for determining the authenticity of food labels for bovine collagen peptides.

Exploring the influence and mechanism of different frying methods on the flavor quality of low-salt sour meat.

To obtain nutritious, healthy, and flavor-enriched sour meat products, the effects of different frying methods (microwave, air-frying, and traditional frying) on the flavor quality of low-salt sour meat were evaluated using metabolomics and other flavor analysis techniques. The pH value of the sour meat rose dramatically, while the TBARS value dropped significantly after frying. E-nose and E-tongue results showed that air-frying could reduce acidity and improve umami. The comprehensive analysis of all samples revealed the identification of 107 volatile flavor compounds, including 10 unique aroma compounds that were specifically detected in the AF group. Additionally, the air frying process notably increased the free amino acid and nucleotide concentrations in sour meat by 53.58% and 159.29%, respectively, while causing a significant reduction in both fatty acid and lactic acid content by 22.84% and 49.29%, respectively. All three frying methods altered the flavor of the samples, but air frying performed better in terms of flavor and texture.

Non-destructive prediction of yak meat freshness indicator by hyperspectral techniques in the oxidation process.

This study examined the potential of hyperspectral techniques for the rapid detection of characteristic indicators of yak meat freshness during the oxidation of yak meat. TVB-N values were determined by significance analysis as the characteristic index of yak meat freshness. Reflectance spectral information of yak meat samples (400-1000 nm) was collected by hyperspectral technology. The raw spectral information was processed by 5 methods and then principal component regression (PCR), support vector machine regression (SVR) and partial least squares regression (PLSR) were used to build regression models. The results indicated that the full-wavelength based on PCR, SVR, and PLSR models were shown greater performance in the prediction of TVB-N content. In order to improve the computational efficiency of the model, 9 and 11 characteristic wavelengths were selected from 128 wavelengths by successive projection algorithm (SPA) and competitive adaptive reweighted sampling (CARS), respectively. The CARS-PLSR model exhibited excellent predictive power and model stability.

Mechanisms of cooking methods on flavor formation of Tibetan pork.

To obtain flavor-enriched Tibetan pork products, the impact of oxidation degree on the flavor of Tibetan pork with different cooking methods (microwaving, frying, boiling, and air frying) was evaluated using an E-nose, an E-tongue, GC-MS, and LC-MS. The level of oxidation was lower in M and F and higher in B and AF groups. Hexanal, pentanal, benzaldehyde, 1-octen-3-ol, and 3-hydroxy-2-butanone were identified as significant contributors to cooked samples. The volatile abundance of microwaved, fried, boiled, and air-fried pork was 1.61, 1.22, 1.47, and 1.69 times higher than raw, respectively. Leucine and threonine were detected to be the highest in the AF group, which were 1.30 and 3.60 times greater than RAW, respectively. In summary, oxidation of lipids and proteins caused by cooking treatments was the main source of flavor in cooked Tibetan pork. Air-frying treatment could greatly promote the production of flavor compounds and give unique flavor to Tibetan pork.

Parallel evolution of two AIM24 protein subfamilies and their conserved functions in ER stress tolerance in land plants.

Despite decades of efforts in genome sequencing and functional characterization, some important protein families remain poorly understood. In this study, we report the classification, evolution, and functions of the largely uncharacterized AIM24 protein family in plants, including the identification of a novel subfamily. We show that two AIM24 subfamilies (AIM24-A and AIM24-B) are commonly distributed in major plant groups. These two subfamilies not only have modest sequence similarities and different gene structures but also are of independent bacterial ancestry. We performed comparative functional investigations on the two AIM24 subfamilies using three model plants: the moss Physcomitrium patens, the liverwort Marchantia polymorpha, and the flowering plant Arabidopsis thaliana. Intriguingly, despite their significant differences in sequence and gene structure, both AIM24 subfamilies are involved in ER stress tolerance and the unfolded protein response (UPR). In addition, transformation of the AIM24-A gene from P. patens into the AIM24-B null mutant of A. thaliana could at least partially rescue ER stress tolerance and the UPR. We also discuss the role of AIM24 genes in plant development and other cellular activities. This study provides a unique example of parallel evolution in molecular functions and can serve as a foundation for further investigation of the AIM24 family in plants.

Origins of strigolactone and karrikin signaling in plants.

Strigolactones (SLs) and karrikins (KARs) are butenolides that influence multiple aspects of plant growth and development. D14 and KAI2 are members of the α/ß-fold hydrolase superfamily and act as receptors of SLs and KARs, as well as of unidentified endogenous KAI2-ligands (KLs). Phylogenetic analyses suggest that plant KAI2 was derived from bacterial RsbQ via horizontal gene transfer (HGT) before the emergence of streptophytes. The D14/KAI2 and RsbQ proteins share conserved tertiary structures and functional features. In this opinion article, we suggest that the acquisition of RsbQ by plant cells was fundamental to the formation of butenolide sensing systems. Recruitment of additional signal transduction components and gene duplication subsequently led to versatile butenolide signaling systems throughout land plants.

Changes in volatile flavor of yak meat during oxidation based on multi-omics.

Hydroxyl radical system combined with GC-IMS and metabolomics were used to assess the effect of oxidation on the formation of volatile flavor emitted from yak meat. The formation of volatile compounds, including heptanal, octanal, nonanal, 2,3-glutaraldehyde, 3-hydroxy-2-butanone, etc. were promoted by oxidation. Among them, 2,3-pentanedione and 3-hydroxy-2-butanone, etc. maybe contributed most to the overall aroma of yak meat, while octanal, nonanal and benzaldehyde maybe related to the formation of off-odor or acidification. Meanwhile, the content of metabolites such as oleic acid, linoleic acid, etc. fatty acids and 3-dehydromangiferic acid, tyrosine were increased or decreased with the time of oxidation. More importantly, the formation of most flavor components in yak meat during the course of oxidation were related to stearidonic acid, acetylleucine, dehydroshikimate, 6-phosphate-glucose etc. differential metabolic components. Moreover, starch and sucrose metabolism (prediction), and amino acid metabolism (enrichment) etc. pathways maybe related with the process of oxidation.

Exploring the formation mechanism of off-flavor of irradiated yak meat based on metabolomics.

Irradiation's effects on quality, volatile compounds, and differential metabolites of yak meat were studied. Irradiation dose at 3 kGy had no effect on yak meat quality, however irradiation dose at 5 kGy resulted in yak meat quality deterioration as well as considerable irradiated off-flavors. And the level of the off-odor was strongly associated with the irradiation dose, and allyl methyl sulfide, octanal, nonanal, benzaldehyde, and 4-methylthiazole were all significant producers of off-odor. Meanwhile, with the increased of radiation dose, the amounts of cysteine, methionine, proline, linoleic acid, stearic acid changed obviously. The main generation pathway of irradiated off-flavors in yak meat were thought to be cysteine and methionine metabolism, and linoleic acid metabolism. The oxidative decomposition of sulfur-containing amino acids and unsaturated fatty acids may cause the off-flavor of irradiation yak meat. This research established a theoretical foundation for future control systems to prevent flavor quality alterations during irradiation preservation.

Effect of ball milling-assisted glycosylation modification on the structure and foaming property of egg white protein.

The effect of different glycosylation degrees on molecular structure and foaming property of egg white protein (EWP) was investigated using ball milling-assisted glycosylation. The results showed the foaming ability (FA) and foam stability (FS) of EWP improved when the degree of glycosylation was increased. In particular, FA of ball milling-assisted glycosylation of EWP enhanced by 39.9% and 28.8%, and the FS increased by 28.7% and 24.0% compared with EWP and ball milling egg white protein (BE) at 150 min of reaction. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) analysis could reflect the grafting degree of EWP and glucose molecules from the side. When EWP was fully grafted with glucose, endogenous fluorescence and free sulfhydryl groups indicated that tertiary structure of EWP was depolymerized, and Fourier transform infrared spectroscopy showed the secondary structure tended to change from order to disorder. The results of this study indicated that ball milling-assisted glycosylation modification was a practical method to improve the foaming property of EWP. PRACTICAL APPLICATION: EWP has great FA and FS, making it indispensable in the baking industry. In this study, ball milling-assisted glycosylation was used to improve the foaming property of EWP, and the molecular structure of EWP with different degrees of glycosylation was fully resolved. The results demonstrated that ball milling, as a physical pretreatment, can fully unfold the structure of EWP. When sugar molecules were fully grafted, the particle size of EWP reduced, solubility increased, and the stability of system improved, thus enhancing the foaming property of EWP. The results can provide theoretical basis for improving the foaming property of EWP and provide a reference value for its industrial application.

Refined Multiscale Entropy Analysis of Wrist Pulse for Gender Difference in Traditional Chinese Medicine among Young Individuals.

Pulse signal analysis plays an important role in promoting the objectification of traditional Chinese medicine (TCM). Like electrocardiogram (ECG) signals, wrist pulse signals are mainly caused by cardiac activities and are valuable in analyzing cardiac diseases. A large number of studies have reported ECG signals can distinguish gender characteristics of normal healthy subjects using entropy complexity measures, consistently showing more complexity in females than males. No research up to date, however, has been found on examining gender differences with wrist pulse signals of healthy subjects on entropy complexity measures. This paper is aimed to fill in the research gap, which could, in turn, provide a deeper insight into the pulse signal and might identify potential differences between ECG signals and pulse signals. In particular, several complementary entropy measures with corresponding refined composite multiscale versions are established to perform the analysis for the filtered TCM pulse signals. Experimental results reveal that regardless of entropy measures used, there is no statistically significant gender difference in terms of entropy complexity, indicating that the pulse signal holds less gender characteristics than the ECG signal. In view of these findings, wrist pulse signals could be likely to provide different pieces of information to ECG signals. The present study is the first to quantitatively evaluate gender differences in healthy pulse signals with measures of entropy complexity and more importantly; we expect this study could make contribution to the ongoing pulse intelligent diagnosis and objective analysis, further facilitating the modernization of TCM pulse diagnosis.

Fungal Genes in Plants: Impact and Potential Applications.

Although there is accumulating evidence for the role of foreign genes in plant development and adaptation, many issues remain. A recent study by Wang et al. on a gene of fungal origin in wheatgrass disease resistance highlights the potential application of fungal genes in crop improvement and related areas.

A mycorrhizae-like gene regulates stem cell and gametophore development in mosses.

Plant colonization of land has been intimately associated with mycorrhizae or mycorrhizae-like fungi. Despite the pivotal role of fungi in plant adaptation, it remains unclear whether and how gene acquisition following fungal interaction might have affected the development of land plants. Here we report a macro2 domain gene in bryophytes that is likely derived from Mucoromycota, a group that includes some mycorrhizae-like fungi found in the earliest land plants. Experimental and transcriptomic evidence suggests that this macro2 domain gene in the moss Physcomitrella patens, PpMACRO2, is important in epigenetic modification, stem cell function, cell reprogramming and other processes. Gene knockout and over-expression of PpMACRO2 significantly change the number and size of gametophores. These findings provide insights into the role of fungal association and the ancestral gene repertoire in the early evolution of land plants.

Author Correction: A mycorrhizae-like gene regulates stem cell and gametophore development in mosses.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Platinum-loaded mesoporous nickel phosphonate and its electrochemical application for sarcosine detection.

In 2009, Sreekumar found that sarcosine, as an effective biomarker, can be used to identify prostate cancer. However, it is difficult to detect sarcosine in urine or plasma because of its low concentration. In this work, we describe a simple strategy for the preparation of sarcosine biosensor based on platinum-loaded mesoporous nickel phosphonate (Pt/MNP) and subsequently apply it to detect sarcosine. Mesoporous structure could increase the active sites on the MNP surface, which makes the Pt/MNP have excellent electrochemical performance for detecting hydrogen peroxide, one of the enzymatic products, and the sarcosine biosensor exhibited a superior electrochemical performance. The linear range of sarcosine biosensor is from 5 to 40 µM and the sensitivity is 123.51 µA mM-1 cm-2. The limit of detection is estimated to be 0.24 µM (S/N = 3). Additionally, the sarcosine biosensor based on Pt/MNP also shows an excellent performance in the anti-interference test and the real serum sample. This work manifests the potential application of Pt/MNP as a novel biosensor material for sarcosine detection, which could be extended to other oxidase-based detection systems.

Amperometric sarcosine biosensor with strong anti-interference capabilities based on mesoporous organic-inorganic hybrid materials.

Amperometric enzyme biosensors are some of the simplest and cheapest types of medical devices used in the rapid detection of biomarkers that have been developed in the past fifty years. When the concentrations of biomarkers are at micromoles per liter, such as for sarcosine, which was recently discovered as a biomarker for prostate cancer, the response signal of the interferences is huge, and the biosensor is hard to satisfy the requirements of practical applications. In this manuscript, we describe a strategy for synthesizing a surface electronegative organic-inorganic hybrid mesoporous material, which could reduce the interference signal much better than Nafion and Chitosan. We verify that the surface potential of the carrier nanomaterial plays an important role in excluding anionic interferences. We also prepare a sensitive (16.35 µA mM-1), low LOD (0.13 µM) and wide linear range (1-70 µM) amperometric sarcosine biosensor with excellent anti-interference properties. This mesoporous material provides a bio-composite platform for the development of simple amperometric biosensors for detecting micromoles per liter of analytes in serum or urine.

Gene refashioning through innovative shifting of reading frames in mosses.

Early-diverging land plants such as mosses are known for their outstanding abilities to grow in various terrestrial habitats, incorporating tremendous structural and physiological innovations, as well as many lineage-specific genes. How these genes and functional innovations evolved remains unclear. In this study, we show that a dual-coding gene YAN/AltYAN in the moss Physcomitrella patens evolved from a pre-existing hemerythrin gene. Experimental evidence indicates that YAN/AltYAN is involved in fatty acid and lipid metabolism, as well as oil body and wax formation. Strikingly, both the recently evolved dual-coding YAN/AltYAN and the pre-existing hemerythrin gene might have similar physiological effects on oil body biogenesis and dehydration resistance. These findings bear important implications in understanding the mechanisms of gene origination and the strategies of plants to fine-tune their adaptation to various habitats.