Floral scents and fruit aromas are crucial volatile organic compounds (VOCs) in plants. They are used in defense mechanisms, along with mechanisms to attract pollinators and seed dispersers. In ...addition, they are economically important for the quality of crops, as well as quality in the perfume, cosmetics, food, drink, and pharmaceutical industries. Floral scents and fruit aromas share many volatile organic compounds in flowers and fruits. Volatile compounds are classified as terpenoids, phenylpropanoids/benzenoids, fatty acid derivatives, and amino acid derivatives. Many genes and transcription factors regulating the synthesis of volatiles have been discovered. In this review, we summarize recent progress in volatile function, composition, biosynthetic pathway, and metabolism regulation. We also discuss unresolved issues and research perspectives, providing insight into improvements and applications of plant VOCs.
Tanshinones are the bioactive nor-diterpenoid constituents of the Chinese medicinal herb Danshen (Salvia miltiorrhiza). These groups of chemicals have the characteristic furan D-ring, which ...differentiates them from the phenolic abietane-type diterpenoids frequently found in the Lamiaceae family. However, how the 14,16-epoxy is formed has not been elucidated. Here, we report an improved genome assembly of Danshen using a highly homozygous genotype. We identify a cytochrome P450 (CYP71D) tandem gene array through gene expansion analysis. We show that CYP71D373 and CYP71D375 catalyze hydroxylation at carbon-16 (C16) and 14,16-ether (hetero)cyclization to form the D-ring, whereas CYP71D411 catalyzes upstream hydroxylation at C20. In addition, we discover a large biosynthetic gene cluster associated with tanshinone production. Collinearity analysis indicates a more specific origin of tanshinones in Salvia genus. It illustrates the evolutionary origin of abietane-type diterpenoids and those with a furan D-ring in Lamiaceae.
Sepiolite (Sep) and exfoliated graphite nanoplatelets (xGnP) were applied as supporting material and thermal conductive fillers to solve the problems of possible leakage, low thermal conductivity and ...high supercooling of m-erythritol (ME) as a phase change material (PCM). The loading of ME in the ME/Sep form-stable PCMs could attain 56 wt% when the Sep was treated by 2.5 M HCl and heated at 800 °C for 1 h. The form-stable PCMs were basically physical mixtures though there were some interactions occurred between the hydroxyl groups of ME and Sep. The thermal stability of ME was improved after it was confined in the supporting materials. In addition, the thermal conductivity of the ME/Sep/xGnP form-stable PCM containing 56% ME and 8.0 wt% xGnP could be enhanced to 0.756 W/mK, which was 103% higher than the corresponding ME/Sep form-stable PCM. Moreover, the transient temperature response of the form-stable PCMs was greatly improved by Sep and xGnP. Furthermore, the supercooling of ME could be decreased from 80 °C for pure ME to about 30 °C in the ME/Sep/xGnP form-stable PCM containing 56% ME and 8.0 wt% xGnP. Besides, the latent heat recovery ratio of the ME/Sep/xGnP form-stable PCMs were also greatly improved.
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•Erythritol/Sep/xGnP form-stable phase change materials were prepared.•The supercooling of ME was suppressed from 80 °C to 30 °C in the form-stable PCM.•The thermal conductivity of the form-stable PCMs was doubled by 8 wt% xGnP.•The thermal stability of ME was increased in the form-stable PCMs.•The ΔHc of ME in the form-stable PCM was close to its ΔHm.
Previous studies have demonstrated associations of perfluoroalkyl substances (PFASs), a group of highly persistent chemicals ubiquitous in wildlife and humans, with hypertension, but the ...relationships are mixed. Furthermore, academic literature on the relationship between isomers of PFASs and blood pressure (BP) and hypertension in populations from a higher pollution area is scant. We studied 1612 Chinese adults, ages 22–96years old, from Shenyang, China, utilizing high performance liquid chromatography-mass spectrometry to analyze isomers of perfluorooctanesulfonate (PFOS), perfluorooctanoate (PFOA), and other PFASs in blood serum. We used a mercury sphygmomanometer to measure BP. Hypertension was defined as a mean systolic BP (SBP) of at least 140mmHg, and/or diastolic BP (DBP) of at least 90mmHg, and/or use of antihypertensive medications. The results showed that increased serum concentrations of all (both branched and linear) isomers of PFASs were associated with higher prevalence of hypertension. Adjusted odds ratios for hypertension per ln-unit (ng/mL) increase in PFASs ranged from 1.10 (95%CI: 1.04, 1.17) for perfluorobutanoic acid (PFBA) to 1.26 (95%CI: 1.12, 1.42) for 3+4+5m PFOS, and the estimated increases in mean SBP and DBP ranged from 0.80mmHg (95%CI: 0.25, 1.34) for PFBA to 4.51mmHg (95%CI: 3.52, 5.51) for 3+4+5m PFOS, and from 0.51mmHg (95%CI: 0.01, 1.01) for perfluorodecanesulfonate (PFDS) to 2.48 (1.80, 3.16) for perfluorononanoic acid (PFNA), respectively. Compared with linear PFASs isomers, we identified more and stronger associations among branched PFASs isomers and blood pressure. Furthermore, females exhibited consistently stronger effects than males. In conclusion, this study is the first of its kind to show that not only PFASs positively associated with elevated blood pressure, but also that branched PFAS isomers are more frequently associated with blood pressure than linear PFAS isomers.
Branched PFASs isomers show greater impact on blood pressure than linear PFASs. Display omitted
•Few studies explored the associations between isomeric PFASs and blood pressure in human.•Branched PFASs isomers show greater impact on blood pressure than linear PFASs.•More associations of PFASs with hypertension were found in females than in males.
Background
Mg is a macronutrient for plant growth. Mg deficiency has become an important limiting factor in intensive agricultural production, resulting in reduced crop yield and quality. Given that ...Mg is also essential for human and animals’ diets, Mg nutrition in plants has become an important issue not only for food security but also for human health.
Scope
We review recent progress in physiological and molecular mechanisms underlying Mg biological functionality, as well as Mg transport and Mg deficiency symptoms in plants.
Conclusions
As both a structural component and a regulatory factor, Mg helps plants achieve higher photosynthetic efficiency, nitrogen use efficiency and stress resistance. Plants need a certain range of Mg concentration for their growth, and a number of key genes responsible for Mg uptake, translocation and detoxification have been identified. Despite its functional importance, basic researches on Mg nutrition are still scarce. A deeper investigation of the genetic and molecular mechanisms employed in Mg nutrition will help to improve crop yield and intensify Mg application in the field. Developing more approaches to enhance Mg concentration in crop edible parts is urgently required for human diet and health.
Machine learning and in particular deep learning (DL) are increasingly important in mass spectrometry (MS)-based proteomics. Recent DL models can predict the retention time, ion mobility and fragment ...intensities of a peptide just from the amino acid sequence with good accuracy. However, DL is a very rapidly developing field with new neural network architectures frequently appearing, which are challenging to incorporate for proteomics researchers. Here we introduce AlphaPeptDeep, a modular Python framework built on the PyTorch DL library that learns and predicts the properties of peptides ( https://github.com/MannLabs/alphapeptdeep ). It features a model shop that enables non-specialists to create models in just a few lines of code. AlphaPeptDeep represents post-translational modifications in a generic manner, even if only the chemical composition is known. Extensive use of transfer learning obviates the need for large data sets to refine models for particular experimental conditions. The AlphaPeptDeep models for predicting retention time, collisional cross sections and fragment intensities are at least on par with existing tools. Additional sequence-based properties can also be predicted by AlphaPeptDeep, as demonstrated with a HLA peptide prediction model to improve HLA peptide identification for data-independent acquisition ( https://github.com/MannLabs/PeptDeep-HLA ).
In tandem mass spectrometry (MS/MS)-based proteomics, search engines rely on comparison between an experimental MS/MS spectrum and the theoretical spectra of the candidate peptides. Hence, accurate ...prediction of the theoretical spectra of peptides appears to be particularly important. Here, we present pDeep, a deep neural network-based model for the spectrum prediction of peptides. Using the bidirectional long short-term memory (BiLSTM), pDeep can predict higher-energy collisional dissociation, electron-transfer dissociation, and electron-transfer and higher-energy collision dissociation MS/MS spectra of peptides with >0.9 median Pearson correlation coefficients. Further, we showed that intermediate layer of the neural network could reveal physicochemical properties of amino acids, for example the similarities of fragmentation behaviors between amino acids. We also showed the potential of pDeep to distinguish extremely similar peptides (peptides that contain isobaric amino acids, for example, GG = N, AG = Q, or even I = L), which were very difficult to distinguish using traditional search engines.
Abstract
Glycine decarboxylase (GLDC) is a key enzyme of glycine cleavage system that converts glycine into one-carbon units. GLDC is commonly up-regulated and plays important roles in many human ...cancers. Whether and how GLDC is regulated by post-translational modifications is unknown. Here we report that mechanistic target of rapamycin complex 1 (mTORC1) signal inhibits GLDC acetylation at lysine (K) 514 by inducing transcription of the deacetylase sirtuin 3 (SIRT3). Upon inhibition of mTORC1, the acetyltransferase acetyl-CoA acetyltransferase 1 (ACAT1) catalyzes GLDC K514 acetylation. This acetylation of GLDC impairs its enzymatic activity. In addition, this acetylation of GLDC primes for its K33-linked polyubiquitination at K544 by the ubiquitin ligase NF-X1, leading to its degradation by the proteasomal pathway. Finally, we find that GLDC K514 acetylation inhibits glycine catabolism, pyrimidines synthesis and glioma tumorigenesis. Our finding reveals critical roles of post-translational modifications of GLDC in regulation of its enzymatic activity, glycine metabolism and tumorigenesis, and provides potential targets for therapeutics of cancers such as glioma.
Abstract
Single‐cell proteomics aims to characterize biological function and heterogeneity at the level of proteins in an unbiased manner. It is currently limited in proteomic depth, throughput, and ...robustness, which we address here by a streamlined multiplexed workflow using data‐independent acquisition (mDIA). We demonstrate automated and complete dimethyl labeling of bulk or single‐cell samples, without losing proteomic depth. Lys‐N digestion enables five‐plex quantification at MS1 and MS2 level. Because the multiplexed channels are quantitatively isolated from each other, mDIA accommodates a reference channel that does not interfere with the target channels. Our algorithm RefQuant takes advantage of this and confidently quantifies twice as many proteins per single cell compared to our previous work (Brunner
et al
, PMID 35226415), while our workflow currently allows routine analysis of 80 single cells per day. Finally, we combined mDIA with spatial proteomics to increase the throughput of Deep Visual Proteomics seven‐fold for microdissection and four‐fold for MS analysis. Applying this to primary cutaneous melanoma, we discovered proteomic signatures of cells within distinct tumor microenvironments, showcasing its potential for precision oncology.
Synopsis
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A robust and automated multiplexed DIA (mDIA) workflow is presented, using complete dimethyl labeling for bulk or single‐cell proteomics. Accurate quantification with a reference channel, combined with the RefQuant algorithm, confirms the hypothesis of a stable single‐cell proteome.
Five‐plex quantification at MS1 and MS2 level for multiplexed DIA is enabled by the Lys‐N enzyme.
A reference channel in mDIA doubles proteomic depth in single cells at 80 single cells per day.
mDIA is combined with Deep Visual Proteomics (DVP) for precision oncology.
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