scholarly journals Single-Molecule Long-Read Sequencing of Purslane (Portulaca oleracea) and Differential Gene Expression Related with Biosynthesis of Unsaturated Fatty Acids

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 655
Author(s):  
Hongmei Du ◽  
Shah Zaman ◽  
Shuiqingqing Hu ◽  
Shengquan Che
Keyword(s):  
Fatty Acids ◽  
Differential Expression ◽  
Single Molecule ◽  
Unsaturated Fatty Acids ◽  
Average Length ◽  
Expression Profiles ◽  
Portulaca Oleracea ◽  
Pcr Analysis ◽  
Sequence Information ◽  
Leaves And Roots

This study aimed to obtain the full-length transcriptome of purslane (Portulaca oleracea); assorted plant samples were used for single-molecule real-time (SMRT) sequencing. Based on SMRT, functional annotation of transcripts, transcript factors (TFs) analysis, simple sequence repeat analysis and long non-coding RNAs (LncRNAs) prediction were accomplished. Total 15.33-GB reads were produced; with 9,350,222 subreads and the average length of subreads, 1640 bp was counted. With 99.99% accuracy, after clustering, 132,536 transcripts and 78,559 genes were detected. All unique SMART transcripts were annotated in seven functional databases. 4180 TFs (including transcript regulators) and 7289 LncRNAs were predicted. The results of RNA-seq were confirmed with qRT–PCR analysis. Illumina sequencing of leaves and roots of two purslane genotypes was carried out. Amounts of differential expression genes and related KEGG pathways were found. The expression profiles of related genes in the biosynthesis of unsaturated fatty acids pathway in leaves and roots of two genotypes of purslane were analyzed. Differential expression of genes in this pathway built the foundation of ω-3 fatty acid accumulation in different organs and genotypes of purslane. The aforementioned results provide sequence information and may be a valuable resource for whole-genome sequencing of purslane in the future.

scholarly journals A kinetic rationale for functional redundancy in fatty acid biosynthesis

2020 ◽  
Vol 117 (38) ◽  
pp. 23557-23564
Author(s):  
Alex Ruppe ◽  
Kathryn Mains ◽  
Jerome M. Fox
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Fatty Acid Synthase ◽  
Unsaturated Fatty Acids ◽  
Fatty Acid Biosynthesis ◽  
Average Length ◽  
Functional Redundancy ◽  
Experimental Investigations ◽  
Total Production

Cells build fatty acids with biocatalytic assembly lines in which a subset of enzymes often exhibit overlapping activities (e.g., two enzymes catalyze one or more identical reactions). Although the discrete enzymes that make up fatty acid pathways are well characterized, the importance of catalytic overlap between them is poorly understood. We developed a detailed kinetic model of the fatty acid synthase (FAS) ofEscherichia coliand paired that model with a fully reconstituted in vitro system to examine the capabilities afforded by functional redundancy in fatty acid synthesis. The model captures—and helps explain—the effects of experimental perturbations to FAS systems and provides a powerful tool for guiding experimental investigations of fatty acid assembly. Compositional analyses carried out in silico and in vitro indicate that FASs with multiple partially redundant enzymes enable tighter (i.e., more independent and/or broader range) control of distinct biochemical objectives—the total production, unsaturated fraction, and average length of fatty acids—than FASs with only a single multifunctional version of each enzyme (i.e., one enzyme with the catalytic capabilities of two partially redundant enzymes). Maximal production of unsaturated fatty acids, for example, requires a second dehydratase that is not essential for their synthesis. This work provides a kinetic, control-theoretic rationale for the inclusion of partially redundant enzymes in fatty acid pathways and supplies a valuable framework for carrying out detailed studies of FAS kinetics.

scholarly journals Chemical Characterization and DNA Fingerprinting of Griffonia simplicifolia Baill.

Molecules ◽  
2019 ◽  
Vol 24 (6) ◽  
pp. 1032 ◽  
Author(s):  
Ivano Vigliante ◽  
Giuseppe Mannino ◽  
Massimo Maffei
Keyword(s):  
Fatty Acids ◽  
Dna Fingerprinting ◽  
Unsaturated Fatty Acids ◽  
Saturated Fatty Acids ◽  
Pcr Analysis ◽  
Chemical Components ◽  
Major Band ◽  
Griffonia Simplicifolia ◽  
Unequivocal Identification ◽  
Pcr Rflp

Background: Griffonia simplicifolia Baill. (Caesalpiniaceae) is a medicinal plant whose seeds are widely used in traditional medicine for their high content of 5-hydroxy-l-tryptophan (5-HTP), a direct precursor and enhancer of the activity of the brain hormone serotonin (5-HT). The plant extracts are used in dietary supplements aimed to alleviate serotonin-related disorders. Methods: In order to characterize the chemical components of G. simplicifolia seeds and their identity, we used a combined methodology by using HPLC-DAD-ESI-MS/MS for the qualitative and quantitative determination of the N-containing compounds, GC-FID and GC-MS for the characterization of the major fatty acids, and DNA fingerprinting based on PCR–RFLP for the unequivocal identification of the plant. Results: 5-HTP was the most representative compound, followed by lower percentages of the β-carboline alkaloid derivative griffonine and other alkaloids. Fatty acids were dominated by the unsaturated fatty acids linoleic acid and oleic acid, followed by the saturated fatty acids stearic and palmitic acids. PCR analysis of the internal transcribed spacer amplified sequence showed a major band at about 758 bp, whereas the PCR–RFLP analysis of this sequence using three different restriction enzymes (MspI, HhaI, and HaeIII) generated a specific fingerprinting useful for the plant identification. Conclusions: The combined chemical and molecular analysis of G. simplicifolia provided an interesting integrated approach for the unequivocal identification of commercial G. simplicifolia seeds.

NALP7 and NALP11 Differential Expression Correlates with Glucocorticoid Sensitivity in Multiple Myeloma Cell Lines.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2366-2366
Author(s):  
Shuo Ma ◽  
Nancy L. Krett ◽  
Steven T. Rosen
Keyword(s):  
Multiple Myeloma ◽  
Differential Expression ◽  
Expression Profiles ◽  
Growth Arrest ◽  
Biological Significance ◽  
Pcr Analysis ◽  
Mrna Levels ◽  
Dependent Manner ◽  
Myeloma Cells ◽  
Transfected Cells

Abstract Multiple myeloma is the second most common hematological malignancy and remains incurable. Glucocorticoids (GC) are among the most commonly used therapy for myeloma by inducing growth arrest and apoptosis in myeloma cells. While GC treatments are usually effective at first, all patients will eventually develop resistance. Understanding the mechanism of GC resistance is an important step towards developing new therapy to overcome this significant clinical problem. In order to study the mechanism underlying the GC resistance phenotype in myeloma, we compared the gene expression profiles of the clinically relevant myeloma clones derived from the same patient (MM.1) which are either sensitive or resistant to GC-induced apoptosis and growth inhibition. By cDNA microarray analysis, we identified NALP7 and NALP11 among the few genes that showed most significant differential levels of expression between the sensitive and resistant myeloma lines. Both genes belong to the NALP (NATCH-, LRR- and pyrin domain-containing proteins) family of proteins which have been implicated in the innate immune response. However, their function and regulation in myeloma has never been explored. Using a two-step quantitative real-time RT-PCR analysis, we have demonstrated that the NALP7 expression was significantly reduced whereas the NALP11 expression was markedly increased in GC-resistant MM.1 cells compared to the GC-sensitive MM.1 cells. We then investigated the biological significance of NALP gene differential expression in myeloma GC-resistance. To test whether suppressing NALP7 expression would lead to GC-resistance, we transfected the sensitive MM.1 cells with NALP-7 siRNA which effectively knocked down NALP7 mRNA level by over 80%. The knock-down of NALP-7, however, did not appear to affect the GC sensitivity of the transfected myeloma cells as dexamethasone (dex) treatment effectively caused growth arrest and apoptosis in transfected cells as in the control cells. We have also tested whether suppressing NALP11 expression would overcome the resistance to GC treatment by transfecting the GC-resistant MM.1 cells with NALP11 siRNA. While NALP11 expression was effectively knocked down to less than 20%, the transfected cells remain resistant to GC treatment as in the control cells, suggesting that NALP11 expression is not required to maintain the GC-resistant phenotype. We further investigated the upstream signaling cascades influencing NALP7 and NALP11 expression. Interestingly, dex treatment suppressed the expression of both NALP7 and NALP11 genes in the GC-sensitive MM.1 cells in a time- and dose-dependent manner. Co-treatment with glucocorticoid receptor (GR) antagonist RU486 blocked the down-regulation of NALP7 and NALP11 by dex, suggesting that a functional GR is required to mediate this action. In GC-resistant MM.1 cells which have much reduced levels of wild type GR, NALP7 and NALP11 mRNA levels were not affected by dex treatment, suggesting further that the suppression of NALP7 by GC requires sufficient levels of GR. Our studies demonstrated that the differential expression of two NALP family genes, NALP7 and NALP11, correlates with GC sensitivity in myeloma, and that both genes are regulated by glucocorticoid signaling. The biological significance of their differential regulation in myeloma remains to be determined.

Relationship between stearoyl-CoA desaturase 1 gene expression, relative protein abundance, and its fatty acid products in bovine tissues

2014 ◽  
Vol 81 (3) ◽  
pp. 333-339 ◽  
Author(s):  
Pedram Rezamand ◽  
Jason S Watts ◽  
Katherine M Yavah ◽  
Erin E Mosley ◽  
Liying Ma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fatty Acids ◽  
Fatty Acid ◽  
Mrna Expression ◽  
Unsaturated Fatty Acids ◽  
Vaccenic Acid ◽  
Mammary Tissue ◽  
Pcr Analysis ◽  
Stearoyl Coa Desaturase ◽  
The Relationship

Stearoyl-CoA desaturase 1 (SCD1) greatly contributes to the unsaturated fatty acids present in milk and meat of cattle. The SCD1 enzyme introduces a double bond into certain saturated fatty acyl-CoAs producing monounsaturated fatty acids (MUFA). The SCD1 enzyme also has been shown to be active in the bovine mammary gland converting t11 18 : 1 (vaccenic acid) to c9 t11 conjugated linoleic acid (CLA). The objective of this study was to determine any association between the gene expression of SCD1 and occurrence of its products (c9 14 : 1, c9 16 : 1, c9 18 : 1, and c9 t11 18 : 2) in various bovine tissues. Tissue samples were obtained from lactating Holstein cows (n=28) at slaughter, frozen in liquid nitrogen and stored at −80 °C. Total RNA was extracted and converted to complementary DNA for quantitative real time polymerase chain reaction (PCR) analysis of the SCD1 gene. Extracted lipid was converted to fatty acid methyl esters and analysed by GC. Tissues varied in expression of SCD1 gene with mammary, cardiac, intestinal adipose, and skeletal muscle expressing greater copy number as compared with lung, large intestine, small intestine and liver (371, 369, 328, 286, 257, 145, 73, and 21 copies/ng RNA, respectively). Tissues with high mRNA expression of SCD1 contained greater SCD1 protein whereas detection of SCD1 protein in tissues with low SCD1 mRNA expression was very faint or absent. Across tissues, the desaturase indices for c9 18 : 1 (r=0·24) and sum of SCD products (r=0·20) were positively correlated with SCD1 gene expression (P<0·01 for both). Within each tissue, the relationship between SCD1 gene expression and the desaturase indices varied. No correlation was detected between SCD1 expression and desaturase indices in the liver, large and small intestines, lung, cardiac or skeletal muscles. Positive correlations, however, were detected between SCD1 expression and the desaturase indices in intestinal adipose tissue (P<0·02 for all) except 14 : 1, whereas only c9 18 : 1, c9 t11 18 : 2 and sum of all desaturase indices were positively correlated with SCD1 expression in mammary tissue (P⩽0·03). Overall, the relationship between SCD1 gene expression and occurrence of its products seems to be tissue specific.

scholarly journals Optimization of Purslane Plant Using Cooking and Pickling Processes for Reducing Oxalate Conten

2018 ◽  
Vol 8 ◽  
pp. 1384-1398
Author(s):  
Waleed Z Badawy ◽  
Salwa G Arafa ◽  
Mihaly Czako
Keyword(s):  
Fatty Acids ◽  
Unsaturated Fatty Acids ◽  
Soluble Fraction ◽  
Radical Scavenging Activity ◽  
Radical Scavenging ◽  
Quality Characteristics ◽  
Portulaca Oleracea ◽  
Total Phenolic ◽  
Scavenging Activity ◽  
Edible Plant

Purslane (Portulaca oleracea) is an edible plant rich in benefcial nutrients. Therefore, this study aimed to determine the chemical composition, minerals, fatty acid analysis, phenolic compounds and radical scavenging activity of purslane plant. In addition, the effect of cooking of purslane at different temperatures (60, 80 and 100 °C), for various durations (5, 10, 15 and 20 minute), and pickling for various durations (3, 6 and 9 days) on oxalate content. Sensory evaluation of quality characteristics and fatty acids analysis of biscuits fortified by purslane powder after reducing oxalate content were carried out. Protein, fat, ash and fiber contents of purslane were 5.64, 5.30, 23.42 and 16.03 %, respectively on dry matter basis. The highest concentration mineral was K (4694.0 mg/100g), while the lowest concentration mineral was Zn (0.93 mg/100g). Total phenolic and radical scavenging activity of purslane were 193.22 mg/100g gallic acid equivalent and 87.29 %, respectively. Purslane contains high percentage of unsaturated fatty acids, especially linolenic acid (40.4 % of total fatty acids). On the other hand, the soluble fraction of total oxalate content of purslane cooked for 20 minutes at 60, 80 and 100 °C were 34.65, 19.84 and 15.84 %, respectively. While, the soluble fraction of total oxalate content of purslane pickled for 0, 3, 6 and 9 days were 47.80, 36.23, 25.60 and 14.39 %, respectively. Fortification of biscuits using purslane powder after treatments led to improvement of the quality characteristics of product. Portulaca oleracea could be used as a good source of minerals, antioxidants and omega-3 especially for functional food and nutraceutical applications.

De novo transcriptome profiling of mustard aphid (Lipaphis erysimi) and differential expression of transcripts associated with developmental stages, feeding and non-feeding conditions

2019 ◽  
Author(s):  
Rubina Chongtham ◽  
Kirti Kulkarni ◽  
Rohit Nandan Shukla ◽  
Gopal Joshi ◽  
Amar Kumar ◽  
...  
Keyword(s):  
Differential Expression ◽  
Target Genes ◽  
Developmental Stages ◽  
De Novo ◽  
Average Length ◽  
Indian Subcontinent ◽  
Expression Profiles ◽  
Lipaphis Erysimi ◽  
Adult Feeding ◽  
Aphid Control

AbstractLipaphis erysimi is a Brassicaceae specialist aphid, which causes significant losses in yield and/or reduction of oil content of vegetable and oilseed brassicas and is a major pest in the Indian subcontinent. This study reports the de novo transcriptome of L. erysimi for the first time. We also present a comparative analysis of nymphs and adult transcriptomes to study the differential expression profiles associated with different developmental stages as well as different feeding conditions. For this, RNA-seq was performed on three different biological samples adults, nymphs (with all nymph stages pooled) and adults starved for 3 hours (referred to as Adult Feeding, AF; Nymphs Feeding, NF, and Adult Starved_3 hr, ANF samples henceforth). A final transcriptome comprising 52,652 transcripts of 1064bp average length and N50 value of 1806 bp was generated. A total of 27,112 transcripts were annotated with insect proteins from SwissProt, of which 4128 transcripts were components of 165 KEGG pathways. A total of 17,296 transcripts were classified based on their Gene Ontology. Potential transcripts for host selection, detoxification, salivary proteins and effectors, molecular chaperones and developmental genes were identified. A total of 23,532 transcripts that remained unannotated were subjected to BLAST against aphid sequences available at AphidBase and a total of 3091 transcripts had hits with sequences of other aphids in the database, out of which 1380 had protein hits. A total of 20441 found to share no homology to any sequence available in the public domain and could therefore represent novel aphid genes or sequences that are unique to L. erysimi. This is an exploratory study with no biological replicates. However, the significant repertoire of feeding- and development-related genes and their differential expression profiles generated in this study adds to the limited data available on L. erysimi and it would facilitate studies on the molecular basis of aphid feeding and development. This could also allow identification of novel target genes for development of RNAi-based aphid control methods.

Genome-wide identification of the AP2/ERF transcription factor family in pepper (Capsicum annuum L.)

Genome ◽  
2018 ◽  
Vol 61 (9) ◽  
pp. 663-674 ◽  
Author(s):  
Jing-Hao Jin ◽  
Min Wang ◽  
Huai-Xia Zhang ◽  
Abid Khan ◽  
Ai-Min Wei ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Differential Expression ◽  
Expression Profiles ◽  
Phytophthora Capsici ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Promoter Regions ◽  
Genome Database ◽  
Cis Acting ◽  
Biotic Stresses

The AP2/ERF family is one of the largest transcription factor families in the plant kingdom. AP2/ERF genes contributing to various processes including plant growth, development, and response to various stresses have been identified. In this study, 175 putative AP2/ERF genes were identified in the latest pepper genome database and classified into AP2, RAV, ERF, and Soloist subfamilies. Their chromosomal localization, gene structure, conserved motif, cis-acting elements within the promoter region, and subcellular locations were analyzed. Transient expression of CaAP2/ERF proteins in tobacco revealed that CaAP2/ERF064, CaAP2/ERF109, and CaAP2/ERF127 were located in the nucleus, while CaAP2/ERF171 was located in the nucleus and cytoplasm. Most of the CaAP2/ERF genes contained cis-elements within their promoter regions that responded to various stresses (HSE, LTR, MBS, Box-W1/W-box, and TC-rich repeats) and phytohormones (ABRE, CGTCA-motif, and TCA-element). Furthermore, RNA-seq analysis revealed that CaAP2/ERF genes showed differential expression profiles in various tissues as well as under biotic stresses. Moreover, qRT-PCR analysis of eight selected CaAP2/ERF genes also showed differential expression patterns in response to infection with Phytophthora capsici (HX-9) and in response to phytohormones (SA, MeJA, and ETH). This study will provide basic insights for further studies of the CaAP2/ERF genes involved in the interaction between pepper and P. capsici.

scholarly journals Differential Expression Profiles and Functional Analysis of Long Non-coding RNAs in Children With Dilated Cardiomyopathy

2021 ◽  
Vol 9 ◽  
Author(s):  
Dongxiao Cai ◽  
Bo Han ◽  
Wei Sun ◽  
Li Zhang ◽  
Jing Wang ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Dilated Cardiomyopathy ◽  
Differential Expression ◽  
Expression Profile ◽  
Microarray Data ◽  
Expression Profiles ◽  
Interaction Network ◽  
Left Ventricular ◽  
Pcr Analysis ◽  
Non Coding Rnas

Aim: To evaluate the expression profile of long non-coding RNAs (lncRNAs) in different left ventricular function of dilated cardiomyopathy (DCM) in children and explore their possible functions.Methods: The lncRNA microarray experiment was used to determine the differential expression profile of lncRNA in three children with DCM and three healthy volunteers. The functional analysis and the construction of the lncRNA-mRNA interaction network were carried out to study the biological functions. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis was used to verify the microarray data.Results: There were 369 up-regulated lncRNAs identified in the DCM patients (fold change &gt;2, P &lt; 0.05), and 505 down-regulated lncRNAs. Based on target gene prediction and co-expression network construction, 9 differentially expressed lncRNAs were selected for the PCR to verify the accuracy of the microarray data, of which 5 were up-regulated and 4 were down-regulated, and finally proved that 7 of them were consistent with the trend of microarray data results. Four of these lncRNAs had significant differences between the patients with poor cardiac function and patients with improved left ventricle function.Conclusion: LncRNAs may play an important role in pediatric DCM and may provide a new perspective for the pathogenesis, diagnosis, and treatment of this disease.

DEVELOPMENT OF AN EXPERIMENTAL MODEL OF AVITAMINOSIS F

2020 ◽  
Vol 20 (2) ◽  
pp. 38-40
Author(s):  
A. Levitsky ◽  
A. Lapinska ◽  
I. Selivanskaya
Keyword(s):  
Fatty Acids ◽  
Experimental Model ◽  
Unsaturated Fatty Acids ◽  
Saturated Fatty Acids ◽  
Coconut Oil ◽  
The Body ◽  
Regulatory Function ◽  
Omega 3 ◽  
White Rats ◽  
Arachidonic Acids

The article analyzes the role of essential polyunsaturated fatty acids (PUFA), especially omega-3 series in humans and animals. The biosynthesis of essential PUFA in humans and animals is very limited, so they must be consumed with food (feed). Тhe ratio of omega-3 and omega-6 PUFA is very important. Biomembranes of animal cells contain about 30% PUFA with a ratio of ω-6/ ω-3 1-2. As this ratio increases, the physicochemical properties of biomembranes and the functional activity of their receptors change. The regulatory function of essential PUFA is that in the body under the action of oxygenase enzymes (cyclooxygenase, lipoxygenase) are formed extremely active hormone-like substances (eicosanoids and docosanoids), which affect a number of physiological processes: inflammation, immunity, metabolism. Moreover, ω-6 PUFA form eicosanoids, which have pro-inflammatory, immunosuppressive properties, and ω-3 PUFAs form eicosanoids and docosanoids, which have anti-inflammatory and immunostimulatory properties. Deficiency of essential PUFA, and especially ω-3 PUFA, leads to impaired development of the body and its state of health, which are manifestations of avitaminosis F. Prevention and treatment of avitaminosis F is carried out with drugs that contain PUFA. To create new, more effective vitamin F preparations, it is necessary to reproduce the model of vitamin F deficiency. An experimental model of vitamin F deficiency in white rats kept on a fat –free diet with the addition of coconut oil, which is almost completely free of unsaturated fatty acids, and saturated fatty acids make up almost 99 % of all fatty acids was developed. The total content of ω-6 PUFA (sum of linoleic and arachidonic acids), the content of ω-3 PUFA (α-linolenic, eicosapentaenoic and docosahexaenoic acids) in neutral lipids (triglycerides and cholesterol esters) defined. Тhe content of ω-6 PUFA under the influence of coconut oil decreased by 3.3 times, and the content of ω-3 PUFA - by 7.5 times. Тhe influence of coconut oil, the content of ω-6 PUFA decreased by 2.1 times, and the content of ω-3 PUFA - by 2.8 times. The most strongly reduces the content of ω-3 PUFA, namely eicosapentaenoic, coconut oil, starting from 5 %. Consumption of FFD with a content of 15 % coconut oil reduces the content of eicosapentaenoic acid to zero, ie we have an absolute deficiency of one of the most important essential PUFAs, which determined the presence of vitamin F deficiency.

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