scholarly journals Gene excavation and expression analysis of CYP and UGT related to the post modifying stage of gypenoside biosynthesis in Gynostemma pentaphyllum (Thunb.) Makino by comprehensive analysis of RNA and proteome sequencing

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260027
Author(s):  
Yangmei Zhang ◽  
Qicong Chen ◽  
Yuanheng Huang ◽  
Ruiqiang Zhao ◽  
Jian Sun ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Expression Analysis ◽  
Biological Activities ◽  
Proteome Analysis ◽  
Absolute Quantification ◽  
Comprehensive Analysis ◽  
Future Research ◽  
Triterpenoid Saponins ◽  
Gynostemma Pentaphyllum ◽  
Isobaric Tags

Previous studies have revealed that gypenosides produced from Gynostemma pentaphyllum (Thunb.) Makino are mainly dammarane-type triterpenoid saponins with diverse structures and important biological activities, but the mechanism of diversity for gypenoside biosynthesis is still unclear. In this study, a combination of isobaric tags for relative and absolute quantification (iTRAQ) proteome analysis and RNA sequencing transcriptome analysis was performed to identify the proteins and genes related to gypenoside biosynthesis. A total of 3925 proteins were identified by proteomic sequencing, of which 2537 were quantified. Seventeen cytochrome P450 (CYP) and 11 uridine 5’-diphospho-glucuronosyltransferase (UDP-glucuronosyltransferase, UGT) candidate genes involved in the side chain synthesis and modification of gypenosides were found. Seven putative CYPs (CYP71B19, CYP77A3, CYP86A7, CYP86A8, CYP89A2, CYP90A1, CYP94A1) and five putative UGTs (UGT73B4, UGT76B1, UGT74F2, UGT91C1 and UGT91A1) were selected as candidate structural modifiers of triterpenoid saponins, which were cloned for gene expression analysis. Comprehensive analysis of RNA sequencing and proteome sequencing showed that some CYPs and UGTs were found at both the transcription and translation levels. In this study, an expression analysis of 7 CYPs and 5 UGTs that contributed to gypenoside biosynthesis and distribution in G. pentaphyllum was performed, providing consistent results that will inspire more future research on vital genes/proteins involved in gypenoside biosynthesis.

scholarly journals A REVIEW OF BOTANY, THERAPEUTIC VALUE, PHYTOCHEMISTRY, AND PHARMACOLOGY OF CUSSONIA PANICULATA

2019 ◽  
pp. 1-6
Author(s):  
ALFRED MAROYI
Keyword(s):  
Herbal Medicine ◽  
Skin Diseases ◽  
Intestinal Parasites ◽  
Biological Activities ◽  
Triterpene Glycosides ◽  
Future Research ◽  
Steroidal Saponin ◽  
Scientific Publications ◽  
Triterpenoid Saponins ◽  
Medicinal Uses

Cussonia paniculata is a small tree widely used as herbal medicine throughout its distributional range in southern Africa. This study is aimed at providing a critical review of the botany, biological activities, phytochemistry, and medicinal uses of C. paniculata. Documented information on the botany, biological activities, medicinal uses, and phytochemistry of C. paniculata was collected from several online sources which included BMC, Scopus, SciFinder, Google Scholar, Science Direct, Elsevier, PubMed, and Web of Science. Additional information on the botany, biological activities, phytochemistry, and medicinal uses of C. paniculata was gathered from pre-electronic sources such as book chapters, books, journal articles, and scientific publications sourced from the University library. This study showed that the bark, fruits, leaves, roots, and stems of C. paniculata are used as emetic, immune booster, and herbal medicine for dysmenorrhea, intestinal parasites and worms, mental problems, boils, shingles and skin diseases, indigestion and stomach complaints, sores, and wounds. Phytochemical compounds identified from the leaves of C. paniculata include acetylated triterpene glycosides, unacetylated triterpene glycosides, flavonoid, steroidal saponin, and triterpenoid saponins. Pharmacological research revealed that C. paniculata extracts have analgesic, antibacterial, anticancer, anti-inflammatory, antiplasmodial, antiprotozoan, Aβ42 protein reduction, and cytotoxicity activities. Future research should focus on evaluating the phytochemical, pharmacological, and toxicological properties of C. paniculata crude extracts as well as compounds isolated from the species.

scholarly journals Protein tyrosine phosphatase receptor type C (PTPRC or CD45)

2021 ◽  
pp. jclinpath-2020-206927
Author(s):  
Maryam Ahmed Al Barashdi ◽  
Ahlam Ali ◽  
Mary Frances McMullin ◽  
Ken Mills
Keyword(s):  
Protein Tyrosine Phosphatase ◽  
Protein Tyrosine Kinase ◽  
Biological Activities ◽  
Tyrosine Phosphatase ◽  
Cell Types ◽  
Receptor Type ◽  
Future Research ◽  
Protein Tyrosine ◽  
Type C ◽  
Almost All

The leucocyte common antigen, protein tyrosine phosphatase receptor type C (PTPRC), also known as CD45, is a transmembrane glycoprotein, expressed on almost all haematopoietic cells except for mature erythrocytes, and is an essential regulator of T and B cell antigen receptor-mediated activation. Disruption of the equilibrium between protein tyrosine kinase and phosphatase activity (from CD45 and others) can result in immunodeficiency, autoimmunity, or malignancy. CD45 is normally present on the cell surface, therefore it works upstream of a large signalling network which differs between cell types, and thus the effects of CD45 on these cells are also different. However, it is becoming clear that CD45 plays an essential role in the innate immune system and this is likely to be a key area for future research. In this review of PTPRC (CD45), its structure and biological activities as well as abnormal expression of CD45 in leukaemia and lymphoma will be discussed.

Chemical Constituents and Biological Activities of Cordia Myxa L.: A Review

2021 ◽  
Vol 11 ◽  
Author(s):  
Varinder Singh ◽  
Ankita Sood ◽  
Simran Pruthi ◽  
Manjinder Singh ◽  
Balraj Saini ◽  
...  
Keyword(s):  
Biological Activities ◽  
Chemical Constituents ◽  
Antimicrobial Activities ◽  
Functional Health ◽  
Future Research ◽  
Health Food ◽  
Toxicological Evaluation ◽  
Cordia Myxa ◽  
Chronic Fever ◽  
Tract Infections

Background: Cordia myxa L. (CM) is a valuable ethnomedicinal plant from Boraginaceae family. Traditionally, CM parts especially fruits and leaves are used in chest and urinary tract infections, diarrhoea, dysentery, tuberculosis, liver and spleen disorders, chronic fever, malaria etc. Objective: Despite of known importance and uses, CM has gained relatively less attention of researchers and concise reviews revealing the medicinal potential of CM are scanty. The present review summarizes the chemical constituents and biological activities of CM and aims to stimulate future research to develop it as a functional health food. Results: Analysis of literature on CM showed that its fruits are a rich source of nutrients and are frequently employed in wide ailments such as urinary and respiratory tract infections, chronic fever, liver disorders, asthma, used as anthelmintic, diuretic, expectorant and purgative. Scientific studies have shown the antidiabetic, analgesic, anti-inflammatory, anti-cancer, antioxidant, antiplasmodial, hepatoprotective, hypotensive, antiulcer and antimicrobial activities of CM. More than 45 compounds belonging to carbohydrates, steroids, carotenoids, phenols, flavonoids and alkaloids have been reported from various parts of CM. Conclusion: Systematic preclinical studies support the traditional claims of CM. The analysis of available literature showed that CM could be developed as a drug. Further, studies such as detailed pharmacological and toxicological evaluation, isolation of bioactive compounds, quantitative phytochemistry and structure activity relationship are scanty and thus, crucial to be addressed for uplifting the scientific value of this revered medicinal plant.

scholarly journals Analysis of conserved miRNAs in cynomolgus macaque genome using small RNA sequencing and homology searching

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9347
Author(s):  
Xia Huang ◽  
Shijia Li ◽  
Xiaoming Liu ◽  
Shuting Huang ◽  
Shuang Li ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Mirna Gene ◽  
Cynomolgus Macaque ◽  
Future Research ◽  
Small Rna Sequencing ◽  
Homology Searching ◽  
Macaque Genome ◽  
Cynomolgus Macaques ◽  
Mirna Clusters

MicroRNAs (miRNAs) are important regulators that fine-tune diverse cellular activities. Cynomolgus macaques (Macaca fascicularis) are used extensively in biomedical and pharmaceutical research; however, substantially fewer miRNAs have been identified in this species than in humans. Consequently, we investigated conserved miRNA profiles in cynomolgus macaques by homology searching and small RNA sequencing. In total, 1,455 high-confidence miRNA gene loci were identified, 408 of which were also confirmed by RNA sequencing, including 73 new miRNA loci reported in cynomolgus macaques for the first time. Comparing miRNA expression with age, we found a positive correlation between sequence conservation and expression levels during miRNA evolution. Additionally, we found that the miRNA gene locations in cynomolgus macaque genome were very flexible. Most were embedded in intergenic spaces or introns and clustered together. Several miRNAs were found in certain gene locations, including 64 exon-resident miRNAs, six splice-site-overlapping miRNAs (SO-miRNAs), and two pairs of distinct mirror miRNAs. We also identified 78 miRNA clusters, 68 of which were conserved in the human genome, including 10 large miRNA clusters predicted to regulate diverse developmental and cellular processes in cynomolgus macaque. Thus, this study not only expands the number of identified miRNAs in cynomolgus macaques but also provides clues for future research on the differences in miRNA repertoire between macaques and humans.

scholarly journals Contribution to the biological interest of Valeriana officinalis: an update

2021 ◽  
Vol 42 ◽  
pp. e67649
Author(s):  
Marta Sánchez ◽  
Elena González-Burgos ◽  
Irene Iglesias ◽  
M. Pilar Gómez-Serranillos Cuadrado
Keyword(s):  
Clinical Trials ◽  
Nervous System ◽  
Biological Activities ◽  
In Vivo Studies ◽  
Neuroprotective Activity ◽  
Future Research ◽  
Valeriana Officinalis ◽  
Valerenic Acid

Valeriana officinalis L. (Caprifoliaceae family) has been traditionally used to treat mild nervous tension and sleep problems. The basis of these activities are mainly attributed to valerenic acid through the modulation of the GABA receptor. Moreover, V. officinalis is claimed to have other biological activities such as cardiovascular benefits, anticancer, antimicrobial and spasmolytic.  The current review aims to update the biological and pharmacological studies (in vitro, in vivo and clinical trials) of V. officinalis and its major secondary metabolites in order to guide future research. Databases PubMed, Science Direct and Scopus were used for literature search including original papers written in English and published between 2014 and 2020. There have been identified 33 articles which met inclusion criteria. Most of these works were performed with V. officinalis extracts and only a few papers (in vitro and in vivo studies) evaluated the activity of isolated compounds (valerenic acid and volvalerenal acid K). In vitro studies focused on studying antioxidant and neuroprotective activity. In vivo studies and clinical trials mainly investigated activities on the nervous system (anticonvulsant activity, antidepressant, cognitive problems, anxiety and sleep disorders). Just few studies were focused on other different activities, highlight effects on symptoms of premenstrual and postmenopausal syndromes. Valeriana officinalis continues to be one of the medicinal plants most used by today's society for its therapeutic properties and whose biological and pharmacological activities continue to arouse great scientific interest as evidenced in recent publications. This review shows scientific evidence on traditional uses of V. officinalis on nervous system.

scholarly journals Effectiveness of aronia berries for reduction of mild fibrosis and gene expression analysis in livers from mice fed a high-fat diet with aronia berries

2016 ◽  
Vol 6 (3) ◽  
pp. 144 ◽  
Author(s):  
Takuya Yamane ◽  
Miyuki Kozuka ◽  
Yoshio Yamamoto ◽  
Yoshihisa Nakano ◽  
Takenori Nakagaki ◽  
...  
Keyword(s):  
Gene Expression ◽  
Liver Fibrosis ◽  
Beneficial Effect ◽  
Rna Sequencing ◽  
Expression Analysis ◽  
High Fat Diet ◽  
Gene Expression Analysis ◽  
High Fat ◽  
Expression Levels ◽  
Beneficial Effects

Background: Aronia berries have many potential effects on health, including an antioxidant effect, effect for antimutagenesis, hepatoprotection and cardioprotection, an antidiabetic effect and inhibition of cancer cell proliferation. Previous human studies have shown that aronia juice may be useful for treatment of obesity disorders.Objective: To reveal relationship between beneficial effect and the gene expression change by aronia berries, we analyzed mice livers using RNA sequencing and RT-qPCR.Method: At 28 days after starting a normal diet, a high fat diet and a high-fat diet containing 10% freeze-dried aronia berries, serum was obtained from veins of mice after isoflurane anesthesia, and liver tissues were isolated and weighed. Triglyceride, total cholesterol and LDL cholesterol levels were measured and total RNAs were extracted. cDNA libraries were prepared according to Illumina protocols and sequenced using an Illumina HiSeq2500 to perform 100 paired-end sequencing. RNA-sequence reads mapping was performed using a DNA nexus. Gene expression analysis was performed. The liver tissue specimens were fixed and embedded in paraffin. After 5-mm-thick paraffin sections had been cut, they were stained with hematoxylin-eosin using the standard procedure and also with Sirius Red.Results: In this study, we found that mild fibrosis induced by a high-fat diet was reduced in livers of mice fed a high-fat diet containing aronia berries. RNA sequencing and RT-qPCR analyses revealed that gene expression levels of Igfbp1 and Gadd45g were increased in livers from mice fed a high-fat diet containing aronia berries. Furthermore, results of an enzyme-linked immunoassay showed that a secreted protein levels of FABP1 and FABP4 were reduced in serum from mice fed a high-fat diet containing aronia berries. The results suggest that aronia berries have beneficial effects on mild fibrosis in liver.Conclusion: Aronia berries have a beneficial effect on liver fibrosis. The recovery from liver fibrosis is associated with expression levels of Gadd45g and Igfbp1 in the liver. The beneficial effects of aronia berries on liver fibrosis reduce the risk of liver cancer diseases and insulin resistance, resulting in reduction of serum FABP1 and FABP4 levels.Keywords: aronia; fibrosis; liver; Igfbp1; Gadd45g

scholarly journals TagSeqTools: a flexible and comprehensive analysis pipeline for NAD tagSeq data

2020 ◽  
Author(s):  
Huan Zhong ◽  
Zongwei Cai ◽  
Zhu Yang ◽  
Yiji Xia
Keyword(s):  
Rna Sequencing ◽  
Comprehensive Analysis ◽  
Enzymatic Reactions ◽  
Computational Tool ◽  
Sequencing Data ◽  
Analysis Pipeline ◽  
Oxford Nanopore ◽  
Long Read ◽  
Identification And Characterization

AbstractNAD tagSeq has recently been developed for the identification and characterization of NAD+-capped RNAs (NAD-RNAs). This method adopts a strategy of chemo-enzymatic reactions to label the NAD-RNAs with a synthetic RNA tag before subjecting to the Oxford Nanopore direct RNA sequencing. A computational tool designed for analyzing the sequencing data of tagged RNA will facilitate the broader application of this method. Hence, we introduce TagSeqTools as a flexible, general pipeline for the identification and quantification of tagged RNAs (i.e., NAD+-capped RNAs) using long-read transcriptome sequencing data generated by NAD tagSeq method. TagSeqTools comprises two major modules, TagSeek for differentiating tagged and untagged reads, and TagSeqQuant for the quantitative and further characterization analysis of genes and isoforms. Besides, the pipeline also integrates some advanced functions to identify antisense or splicing, and supports the data reformation for visualization. Therefore, TagSeqTools provides a convenient and comprehensive workflow for researchers to analyze the data produced by the NAD tagSeq method or other tagging-based experiments using Oxford nanopore direct RNA sequencing. The pipeline is available at https://github.com/dorothyzh/TagSeqTools, under Apache License 2.0.

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