Comparative transcriptomic analysis provides insights into the genetic networks regulating oil differential production in oil crops.

BACKGROUND: Plants differ more than threefold in seed oil contents (SOCs). Soybean (Glycine max), cotton (Gossypium hirsutum), rapeseed (Brassica napus), and sesame (Sesamum indicum) are four important oil crops with markedly different SOCs and fatty acid compositions. RESULTS: Compared to grain crops like maize and rice, expanded acyl-lipid metabolism genes and relatively higher expression levels of genes involved in seed oil synthesis (SOS) in the oil crops contributed to the oil accumulation in seeds. Here, we conducted comparative transcriptomics on oil crops with two different SOC materials. In common, DIHYDROLIPOAMIDE DEHYDROGENASE, STEAROYL-ACYL CARRIER PROTEIN DESATURASE, PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE, and oil-body protein genes were both differentially expressed between the high- and low-oil materials of each crop. By comparing functional components of SOS networks, we found that the strong correlations between genes in "glycolysis/gluconeogenesis" and "fatty acid synthesis" were conserved in both grain and oil crops, with PYRUVATE KINASE being the common factor affecting starch and lipid accumulation. Network alignment also found a conserved clique among oil crops affecting seed oil accumulation, which has been validated in Arabidopsis. Differently, secondary and protein metabolism affected oil synthesis to different degrees in different crops, and high SOC was due to less competition of the same precursors. The comparison of Arabidopsis mutants and wild type showed that CINNAMYL ALCOHOL DEHYDROGENASE 9, the conserved regulator we identified, was a factor resulting in different relative contents of lignins to oil in seeds. The interconnection of lipids and proteins was common but in different ways among crops, which partly led to differential oil production. CONCLUSIONS: This study goes beyond the observations made in studies of individual species to provide new insights into which genes and networks may be fundamental to seed oil accumulation from a multispecies perspective.

Comparison of the Metabolomics of Different Dendrobium Species by UPLC-QTOF-MS.

Dendrobium Sw. (family Orchidaceae) is a renowned edible and medicinal plant in China. Although widely cultivated and used, less research has been conducted on differential Dendrobium species. In this study, stems from seven distinct Dendrobium species were subjected to UPLC-QTOF-MS/MS analysis. A total of 242 metabolites were annotated, and multivariate statistical analysis was employed to explore the variance in the extracted metabolites across the various groups. The analysis demonstrated that D. nobile displays conspicuous differences from other species of Dendrobium. Specifically, D. nobile stands out from the remaining six taxa of Dendrobium based on 170 distinct metabolites, mainly terpene and flavonoid components, associated with cysteine and methionine metabolism, flavonoid biosynthesis, and galactose metabolism. It is believed that the variations between D. nobile and other Dendrobium species are mainly attributed to three metabolite synthesis pathways. By comparing the chemical composition of seven species of Dendrobium, this study identified the qualitative components of each species. D. nobile was found to differ significantly from other species, with higher levels of terpenoids, flavonoids, and other compounds that are for the cardiovascular field. By comparing the chemical composition of seven species of Dendrobium, these qualitative components have relevance for establishing quality standards for Dendrobium.

HS-GC-IMS Analysis of Volatile Organic Compounds in Different Varieties and Harvesting Times of Rhizoma gastrodiae (Tian Ma) in Yunnan Province.

Headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS) coupled with principal component analysis (PCA) was used to investigate the differences in volatile organic compounds (VOCs) in four different varieties of Yunnan Huang Tian Ma (containing both winter and spring harvesting times), Yunnan Hong Tian Ma, Yunnan Wu Tian Ma, and Yunnan Lv Tian Ma. The results showed that the flavor substances of different varieties and different harvesting times of Rhizoma gastrodiae were mainly composed of aldehydes, alcohols, ketones, heterocycles, esters, acids, alkenes, hydrocarbons, amines, phenols, ethers, and nitrile. Among them, the contents of the aldehydes, alcohols, ketones, and heterocyclic compounds are significantly higher than those of other substances. The results of cluster analysis and fingerprint similarity analysis based on principal component analysis and Euclidean distance showed that there were some differences between different varieties of Yunnan Rhizoma gastrodiae and different harvesting times. Among them, Yunnan Lv Tian Ma and Wu Tian Ma contained the richest volatile components. Winter may be the best harvesting season for Tian Ma. At the same time, we speculate that the special odor contained in Tian Ma should be related to the aldehydes it is rich in, especially benzene acetaldehyde, Benzaldehyde, Heptanal, Hexanal, Pentanal, and butanal, which are aldehydes that contain a strong and special odor and are formed by the combination of these aldehydes.

Comparative proteomics of whey proteins: New insights into quantitative differences between bovine, goat and camel species.

Whey proteins are the leading proteins class in milk and play an essential role in the immune defense of neonatal mammals. The aim of this study was to analyze whey proteins in bovine, goat and camel milk by label free proteomics techniques. Finally, 840 proteins were identified, which considerably increasing the number of whey proteins identified in these species. The results of the PCA revealed significant differences in whey proteome patterns between bovine, goat and camel milk. Proteins such as PAEP, CST3, SERPING1, CTSB and GLG1 play an important role as markers in the classification of bovine, goat and camel milk. Statistical analysis showed that the relative abundances of many whey proteins such as ALB, LALBA, LTF and LPO were significantly different among different species. GO and KEGG functional analysis have shown that while the distribution of biological functions involved in whey proteins was relatively similar across species, they differed in terms of protein quantity. These data shed light on the quantitative differences and potential physiological functions of whey proteins across species, and may point the way to the production of specific functional whey proteins.

Quality consistency evaluation on three species of North Patrininae herba by high-performance liquid chromatography coupled with electrospray ion trap time-of-flight mass spectrometry and network pharmacology approaches.

North Patrininae herba, a perennial herbaceous plant, has long been used in traditional Chinese medicine to treat appendicitis, enteritis, and dysentery. Sonchus arvensis L., Sonchus oleraceus L., and Ixeris chinensis (Thunb.) Nakai are used as substitutes for North Patrininae in different regions, but the consistency of chemical composition and efficacy of these three species is still unknown. In this study, a detailed chemical analysis was carried out of the extract obtained from Sonchus arvensis L., Ixeris chinensis (Thunb.) Nakai and Sonchus oleraceus L. and a chemical component not previously reported in Ixeris chinensis (Thunb.) Nakai was found-Luteolin-7-O-(6''-malonylglucoside). The mechanism of action of the extract against inflammation and type II diabetes was investigated using network pharmacology and analysis of blood-absorbed components following oral dosing of rats. Finally, a highly accurate and reliable method was established for quality control purposes. The results showed that Sonchus arvensis L. and Sonchus oleraceus L. may be considered potential resources of a medicinal compound, whereas Ixeris chinensis (Thunb.) Nakai requires further evaluation.

Mesenchymal Stem Cells Transplantation in Intracerebral Hemorrhage: Application and Challenges.

Intracerebral hemorrhage (ICH) is one of the leading causes of death and long-term disability worldwide. Mesenchymal stem cell (MSC) therapies have demonstrated improved outcomes for treating ICH-induced neuronal defects, and the neural network reconstruction and neurological function recovery were enhanced in rodent ICH models through the mechanisms of neurogenesis, angiogenesis, anti-inflammation, and anti-apoptosis. However, many key issues associated with the survival, differentiation, and safety of grafted MSCs after ICH remain to be resolved, which hinder the clinical translation of MSC therapy. Herein, we reviewed an overview of the research status of MSC transplantation after ICH in different species including rodents, swine, monkey, and human, and the challenges for MSC-mediated ICH recovery from pathological microenvironment have been summarized. Furthermore, some efficient strategies for the outcome improvement of MSC transplantation were proposed.

Variation in IgE binding potencies of seven Artemisia species depending on content of major allergens.

BACKGROUND: Artemisia weed pollen allergy is important in the northern hemisphere. While over 350 species of this genus have been recorded, there has been no full investigation into whether different species may affect the allergen diagnosis and treatment. This study aimed to evaluate the variations in amino acid sequences and the content of major allergens, and how these affect specific IgE binding capacity in representative Artemisia species. METHODS: Six representative Artemisia species from China and Artemisia vulgaris from Europe were used to determine allergen amino acid sequences by transcriptome, gene sequencing and mass spectrometry of the purified allergen component proteins. Sandwich ELISAs were developed and applied for Art v 1, Art v 2 and Art v 3 allergen quantification in different species. Aqueous pollen extracts and purified allergen components were used to assess IgE binding by ELISA and ImmunoCAP with mugwort allergic patient serum pools and individual sera from five areas in China. RESULTS: The Art v 1 and Art v 2 homologous allergen sequences in the seven Artemisia species were highly conserved. Art v 3 type allergens in A. annua and A. sieversiana were more divergent compared to A. argyi and A. vulgaris. The allergen content of Art v 1 group in the seven extracts ranged from 3.4% to 7.1%, that of Art v 2 from 1.0% to 3.6%, and Art v 3 from 0.3% to 10.5%. The highest IgE binding potency for most Chinese Artemisia allergy patients was with A. annua pollen extract, followed by A. vulgaris and A. argyi, with A. sieversiana significantly lower. Natural Art v 1-3 isoallergens from different species have almost equivalent IgE binding capacity in Artemisia allergic patients from China. CONCLUSION AND CLINICAL RELEVANCE: There was high sequence similarity but different content of the three group allergens from different Artemisia species. Choice of Artemisia annua and A. argyi pollen source for diagnosis and immunotherapy is recommended in China.

Tubulin-Based DNA Barcode: Principle and Applications to Complex Food Matrices.

The DNA polymorphism diffusely present in the introns of the members of the Eukaryotic beta-tubulin gene families, can be conveniently used to establish a DNA barcoding method, named tubulin-based polymorphism (TBP), that can reliably assign specific genomic fingerprintings to any plant or/and animal species. Similarly, many plant varieties can also be barcoded by TBP. The method is based on a simple cell biology concept that finds a conveniently exploitable molecular basis. It does not depend on DNA sequencing as the most classically established DNA barcode strategies. Successful applications, diversified for the different target sequences or experimental purposes, have been reported in many different plant species and, of late, a new a version applicable to animal species, including fishes, has been developed. Also, the TBP method is currently used for the genetic authentication of plant material and derived food products. Due to the use of a couple of universal primer pairs, specific for plant and animal organisms, respectively, it is effective in metabarcoding a complex matrix allowing an easy and rapid recognition of the different species present in a mixture. A simple, dedicated database made up by the genomic profile of reference materials is also part of the analytical procedure. Here we will provide some example of the TBP application and will discuss its features and uses in comparison with the DNA sequencing-based methods.

Study on Metabolic Differences of Cajanonic Acid A in Different Species of Liver Microsomes by UPLC-MS/MS / 中国药房

OBJECTIVE： To establish a determination method for the concentration of cajanonic acid A （CAA） in liver microsome incubation system， and to compare the metabolism characteristics of it in different species of liver microsomes. METHODS： CAA was dissolved in liver microsome incubation system of rat， Beagle dog and human initiated by reduced nicotinamide adenine dinucleotide phosphate （NADPH）， and was incubated in water at 37 ℃. The reaction was terminated with acetonitrile at 0， 5， 10， 15， 30， 45 and 60 min， respectively. Using genistein as internal standard， the concentration of CAA in  different incubation systems was determined by UPLC-MS/MS. The determination was performed on Waters BEH C18 column with mobile phase consisted of water （containing 0.1％ formic acid）-acetonitrile （containing 0.1％ formic acid） （45 ∶ 55， V/V） at the flow rate of 0.25 mL/min. The column temperature was 30 ℃， and the sample size was 2 μL. The electrospray ionization source was used to the select reaction monitoring mode for negative ion scanning. The ion pairs for quantitative analysis were m/z 353.14→309.11 （CAA）， m/z 269.86→224.11 （internal standard） respectively. The residual percentage and enzymatic kinetic parameters of CAA in different incubation systems were calculated according to the mass concentration of CAA at 0 min. RESULTS： The linear range of CAA was 0.05-20 μg/mL； the limit of quanti- tation was 0.05 μg/mL， and the lowest detection limit was 0.01 μg/mL. RSDs of intra-day and inter-day were lower than 10％； relative errors ranged －4.83％-8.94％； extraction method and matrix effect did not affect the determination of the substance to be measured. At 60 min of incubation， residual percentages of CAA in rat， Beagle dog and human liver microsomes were（62.79±9.99）％，（64.07±11.59）％，（96.66±5.71）％， respectively. The half-life period （72.19， 68.61 min） of CAA in rat and Beagle dog liver microsomes were significantly shorter than human liver microsome （364.74 min）. The clearance rates [0.019 2， 0.020 2 mL/（min·mg）] were significantly higher than human liver microsome [0.003 8 mL/（min·mg）] （P＜0.05）. CONCLUSIONS： Established UPLC-MS/MS method is simple， rapid， specific and sensitive， and can be used for the determination of CAA concentration in liver microsome incubation system and the study of metabolism stability in vitro. The stability of CAA metabolism in rat and Beagle dog liver microsomes are poorer than human liver microsome.

Study on the Metabolic Characteristics of Piperitylmagnolol in Different Species of Liver Microsomes by UPLC-MS/MS / 中国药房

OBJECTIVE： To establish a method for the determination of piperitylmagnolol in the incubation system of liver microsomes， and to investigate the metabolic characteristics of it in different species of liver microsomes. METHODS： The piperitylmagnolol were respectively dissolved in NADPH activated liver microsome incubation systems of human， rat， mouse， monkey and dog， and then incubated in water at 37 ℃. The reaction was terminated with methanol at 0， 2， 5， 10， 15， 20， 30， 45 and 60 minutes of incubation， respectively. Using magnolol as internal standard， UPLC-MS/MS method was used to determine the concentration of piperitylmagnolol in the incubation system. The determination was performed on Acquity UPLCTM CSH C18 column with mobile phase consisted of 0.1％ formic acid-methanol （gradient elution） at the flow rate of 0.3 mL/min. The column temperature was set at 30 ℃， and the sample size was 2 μL. The ion source was electrospray ion source， and the positive ion scanning was carried out in the multiple reaction monitoring mode. The ion pairs used for quantitative analysis were m/z 401.2→331.1 （piperitylmagnolol） and m/z 265.1→247.0 （internal standard）， respectively. Using the concentration of piperitylmagnolol at 0 min of incubation as a reference， the residual percentage， metabolism half-life in vitro （t1/2） and intrinsic clearance （CLint） were calculated for different incubation systems. The metabolic pathway of piperitylmagnolol was studied by chemical inhibitor method. Under the above chromatographic conditions， the metabolites in vitro were preliminarily analyzed by first-order full scanning and positive ion detection. RESULTS： The linear range of piperitylmagnolol was 3.91-500.00 ng/mL. The limit of quantitation was 3.91 ng/mL. RSDs of intra-day and inter-day were less than 10％. The accuracy ranged 87.40％-103.75％. Matrix effect didn’t affect the determination of the substance to be measured. The piperitylmagnolol was metabolized significantly in human， rat， mouse and dog liver microsomes， but not in monkey liver microsomes. After incubating for 30 min， residual percentage of piperitylmagnolol kept stable in different species of liver microsomes. The t1/2 of piperitylmagnolol were 12.07， 17.68， 17.59， 216.56 and 61.88 min in human， rat， mouse， monkey and dog liver microsomes； CLint were 0.115， 0.078， 0.079， 0.006， 0.022 mL/（min·mg）， respectively. Inhibitory rates of CYP2A6， CYP2D6， CYP2C19， CYP3A4， CYP2C9， CYP2E1 and CYP1A2 to compound metabolism were 55.76％， 93.94％， 96.01％， 93.69％， 71.81％， 23.25％， 28.04％， respectively. Quasi-molecular ion peaks of the two main metabolites of piperitylmagnolol in human liver microsomes were m/z 441.2（[M+Na]+） and m/z 337.2（[M+H]+）， respectively. CONCLUSIONS： Established UPLC-MS/MS method is simple， rapid and specific， and can be used for the determination of piperitylmagnolol concentration in the incubation system of liver microsomes and pharmacokinetic study. The metabolic characteristics of the compound are different among liver microsomes of human， rat， mouse， monkey and dog. Its metabolism process may be associated with CYP2D6， CYP2C19， CYP3A4， CYP2C9， etc.

Characterization of different native american physalis species and evaluation of their processing potential as jelly in combination with brie-type cheese

Abstract Faced with the need for greater knowledge of the different physalis species, the aim of this study was to characterize different Native American physalis species (Physalis peruviana L., Physalis pubescens L., Physalis angulata L., Physalis mínimos L. and Physalis ixocarpa Brot) as to their physicochemical characteristics, bioactive compounds and antioxidant activity. Besides that, in order to increase their use and add even more value to this fruit, we also evaluate the influence of these different species on the physicochemical, rheological and sensory characteristics of physalis jelly. In addition, this study evaluated the sensory acceptance of the combination of physalis jellies obtained from different species with brie-type cheese. The Peruviana, Pubences and Angulata, are highlighted for being the nutritionally richest species, with the highest levels of phenolic compounds, vitamin C and antioxidant. Moreover, they stand out for originating the most widely sensory accepted jellies, either in pure form or in combination with brie-type cheese.

Molecular characterization and phylogenetic analysis of Plasmodium vivax, Plasmodium falciparum, Plasmodium ovale, Plasmodium malariae and Plasmodium cynomolgi.

18S ribosomal RNA gene sequences of different species of Plasmodium were aligned and analyzed to determine the molecular diversity among different species of Plasmodium. AT content of P. cynomolgi, P. ovale, P. falciparum, P. vivax and P. malariae ranged from 62.30 to 63.15, 63.90 to 65.29, 66.67 to 68.40, 61.66 to 63.25 and 64.09 to 76.36 in case respectively. GC content of P. cynomolgi, P. ovale, P. falciparum, P. vivaxand P. malariae ranged from 36.85 to 37.70, 34.71 to 36.43, 31.60 to 33.27, 23.64 to 35.91 and 36.75 to 38.34 respectively. Molecular weight (Da) of P. cynomolgi, P. ovale, P. falciparum, P. vivax and P. malariae ranged from 1,160,127.00 to 1,400,332.00, 437,273.00 to 481,438.00, 668,021.00 to 685,243.00, 540,378.00 to 1,176,962.00 and 132,788.00 to 305,211.00 respectively. Relative melting temperature (Tm) of P. cynomolgi and P. ovale varied from 0.36799 to 0.36837 and 0.36712 to 0.36814 respectively. In P. falciparum and P. vivax relative Tm ranged from 0.36545 to 0.36626 and 0.36802 to 0.36866 respectively. Relative Tm of P. malariae varied from 0.36174 to 0.36790.

[Study on characteristic spectrum of ingredients from different species Cordyceps and its anti-fibrotic activity on human embryonic fibroblasts].

In this study, 10 samples of parasites, cursive, and the whole from six different species of Cordyceps were determined and compared by HPLC and LC-MS methods. Uridine, adenosine, and cordycepin were selected as the main evaluation index. The anti-fibrotic activity of different species Cordyceps extracts was observed using in vitro TGF-ß1-induced ECM accumulation in human embryonic fibroblasts CCC-ESF-1. The results demonstrated that the number of atoms and hyphae ingredients of different species showed little difference, however, the content distribution of each component has obvious significance. The in vitro anti-fibrotic activities of different species were as follow： Cordyceps flower > Cicada Cordyceps (Cicada flower)> Silkworm Cordyceps> Tussah Cordyceps>natural Cordyceps. Our preliminary data could serve as reference for the discovery of artificial alternatives of natural Cordyceps.

Study on characteristic spectrum of ingredients from different species Cordyceps and its anti-fibrotic activity on human embryonic fibroblasts / 中国中药杂志

In this study, 10 samples of parasites, cursive, and the whole from six different species of Cordyceps were determined and compared by HPLC and LC-MS methods. Uridine, adenosine, and cordycepin were selected as the main evaluation index. The anti-fibrotic activity of different species Cordyceps extracts was observed using in vitro TGF-β1-induced ECM accumulation in human embryonic fibroblasts CCC-ESF-1. The results demonstrated that the number of atoms and hyphae ingredients of different species showed little difference, however, the content distribution of each component has obvious significance. The in vitro anti-fibrotic activities of different species were as follow： Cordyceps flower > Cicada Cordyceps (Cicada flower)> Silkworm Cordyceps> Tussah Cordyceps>natural Cordyceps. Our preliminary data could serve as reference for the discovery of artificial alternatives of natural Cordyceps.

Associação e distribuição das espécies de peixes na laguna de Marapendi, Rio de Janeiro, no período de março de 1985 a fevereiro de 1987 / Association and distribution of fishes in the Marapendi lagoon, Rio de Janeiro, from March 1985 to February 1987

From March 1985 to February 1987 montly cast net and beach seine sambles were collected at the Marapendi lagoon, Rio de Janeiro, Brazil, to describe its ichthyofauna and analyze associations between species and their distribution in areas with different salinity regimes. A stratified random sampling design was used and the lagoon diveided in four areas (1-4) according to salinity gradient. The "Bravais-Pearson" correlation index was utilized to analyze the similarity between species and between areas and also group them according to the UPGMA method. According to the results eight species groups were established. The majority of the species were wuryhaline, having a marine origin and were distributed in areas 1, 2 and 3 (high salinity areas). The formation of smaller groups with species of fresh water origin, which occurred in areas 2, 3 and 4 is also discussed.