scholarly journals A model system of gene-enzyme nomenclature in the genome era applied to aromatic biosynthesis

2018 ◽  
Author(s):  
Fangfang Xia ◽  
Carol A Bonner ◽  
Roy A Jensen
Keyword(s):  
Amino Acid ◽  
Metabolic Pathways ◽  
Model System ◽  
Gene Products ◽  
Functional Roles ◽  
Aromatic Biosynthesis ◽  
Enzyme Nomenclature ◽  
The Common ◽  
Common Problems ◽  
Aromatic Pathway

Background: The accurate annotation of functional roles for newly sequenced genes of genomes is not a simple matter. Function is, of course, related to amino-acid sequence and to domain structure but not always in straightforward ways. Even where given functional roles have been identified experimentally, the application of an uneven and erratic nomenclature has generated confusion on the part of annotators and has produced errors that tend to become progressively compounded in database repositories. Results: The pathway that is deployed in nature for aromatic biosynthesis exemplifies an accumulation of chaotic nomenclature and a variety of annotation dilemmas. We view this pathway as one that is sufficiently complex to pose most of the common problems, and yet is one that at the same time is of a manageable size. A set of guidelines has been developed for naming genes of aromatic-pathway biosynthesis and the corresponding gene products, and we suggest that these can be generalized for application to other metabolic pathways. Conclusion: A system of nomenclature for aromatic biosynthesis is presented that is logical, consistent, and evolutionarily informative.

scholarly journals A model system of gene-enzyme nomenclature in the genome era applied to aromatic biosynthesis

2018 ◽  
Author(s):  
Fangfang Xia ◽  
Carol A Bonner ◽  
Roy A Jensen
Keyword(s):  
Amino Acid ◽  
Metabolic Pathways ◽  
Model System ◽  
Gene Products ◽  
Functional Roles ◽  
Aromatic Biosynthesis ◽  
Enzyme Nomenclature ◽  
The Common ◽  
Common Problems ◽  
Aromatic Pathway

Background: The accurate annotation of functional roles for newly sequenced genes of genomes is not a simple matter. Function is, of course, related to amino-acid sequence and to domain structure but not always in straightforward ways. Even where given functional roles have been identified experimentally, the application of an uneven and erratic nomenclature has generated confusion on the part of annotators and has produced errors that tend to become progressively compounded in database repositories. Results: The pathway that is deployed in nature for aromatic biosynthesis exemplifies an accumulation of chaotic nomenclature and a variety of annotation dilemmas. We view this pathway as one that is sufficiently complex to pose most of the common problems, and yet is one that at the same time is of a manageable size. A set of guidelines has been developed for naming genes of aromatic-pathway biosynthesis and the corresponding gene products, and we suggest that these can be generalized for application to other metabolic pathways. Conclusion: A system of nomenclature for aromatic biosynthesis is presented that is logical, consistent, and evolutionarily informative.

scholarly journals A Practical Approach to the Investigation of Amino Acid Disorders

1988 ◽  
Vol 25 (2) ◽  
pp. 129-141 ◽  
Author(s):  
M A Edwards ◽  
S Grant ◽  
A Green
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Analysis ◽  
Practical Approach ◽  
The Common ◽  
Common Problems

We have, in this paper, highlighted some of the common problems in amino acid analysis in our experience and listed the possible causes for increases in specific amino acids in urine—together with guidance on appropriate follow-up investigations.

Applying Possessive pronoun in Writing Sentences: Exploring Students’ Ability and Problems in a Mixed Method Study

2019 ◽  
Vol 1 (3) ◽  
pp. 79-83
Author(s):  
Eka Utami Putri ◽  
Syahdan Syahdan
Keyword(s):  
Mixed Method ◽  
Simple Random Sampling ◽  
Average Score ◽  
Mixed Method Study ◽  
Z Score ◽  
Possessive Pronoun ◽  
Efl Students ◽  
The Common ◽  
Common Problems ◽  
Essay Test

The purpose of this research was to find out the students' ability in applying Possessive pronoun in writing sentences and the problems encounter it.  This mixed method study employs an explanatory design to reveals it. 53 students out of 105 students from1st semester EFL students from one reputable University in Pekanbaru, Indonesia, were invited to this study. These 53 students were selected using simple random sampling and enrolled for an essay test and interview to see the students' ability and explaining the problems. The data analysis using SPSS showed that the average score of students was 52.98. Meanwhile for the median is 48, the mode is 20. The score of Standard Deviation is 27.93, Variance is 780.25, and Range is 84.  Z-Score was found 41.5%, which is means higher than average and 58.5% while, students' ability was indicated below the average. It showed that the students were low ability in applying possessive pronoun in writing sentences. The study also found the common problems, i.e., (1) students still mixed up between possessive pronoun and possessive adjectives. (2) students used the wrong pattern in using a possessive pronoun. (3) students did not understand clearly about a possessive pronoun, (4) experiencing difficulties in learning possessive pronoun. 

Measuring the World

2018 ◽  
Author(s):  
Ann-Sophie Barwich
Keyword(s):  
Sensory Information ◽  
Network Models ◽  
Model System ◽  
Stimulus Input ◽  
Expectancy Effects ◽  
Neural Network Models ◽  
Perceptual Object ◽  
External Objects ◽  
The Common ◽  
The Brain

How much does stimulus input shape perception? The common-sense view is that our perceptions are representations of objects and their features and that the stimulus structures the perceptual object. The problem for this view concerns perceptual biases as responsible for distortions and the subjectivity of perceptual experience. These biases are increasingly studied as constitutive factors of brain processes in recent neuroscience. In neural network models the brain is said to cope with the plethora of sensory information by predicting stimulus regularities on the basis of previous experiences. Drawing on this development, this chapter analyses perceptions as processes. Looking at olfaction as a model system, it argues for the need to abandon a stimulus-centred perspective, where smells are thought of as stable percepts, computationally linked to external objects such as odorous molecules. Perception here is presented as a measure of changing signal ratios in an environment informed by expectancy effects from top-down processes.

scholarly journals Itaconate Alters Succinate and Coenzyme A Metabolism via Inhibition of Mitochondrial Complex II and Methylmalonyl-CoA Mutase

Metabolites ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 117
Author(s):  
Thekla Cordes ◽  
Christian M. Metallo
Keyword(s):  
Amino Acid ◽  
Metabolic Pathways ◽  
Mammalian Cells ◽  
Coenzyme A ◽  
Cultured Cells ◽  
Tca Cycle ◽  
Regulatory Function ◽  
Reversible Inhibitor ◽  
Complex Ii ◽  
Branched Chain

Itaconate is a small molecule metabolite that is endogenously produced by cis-aconitate decarboxylase-1 (ACOD1) in mammalian cells and influences numerous cellular processes. The metabolic consequences of itaconate in cells are diverse and contribute to its regulatory function. Here, we have applied isotope tracing and mass spectrometry approaches to explore how itaconate impacts various metabolic pathways in cultured cells. Itaconate is a competitive and reversible inhibitor of Complex II/succinate dehydrogenase (SDH) that alters tricarboxylic acid (TCA) cycle metabolism leading to succinate accumulation. Upon activation with coenzyme A (CoA), itaconyl-CoA inhibits adenosylcobalamin-mediated methylmalonyl-CoA (MUT) activity and, thus, indirectly impacts branched-chain amino acid (BCAA) metabolism and fatty acid diversity. Itaconate, therefore, alters the balance of CoA species in mitochondria through its impacts on TCA, amino acid, vitamin B12, and CoA metabolism. Our results highlight the diverse metabolic pathways regulated by itaconate and provide a roadmap to link these metabolites to potential downstream biological functions.

scholarly journals Comprehensive transcriptome and metabolome profiling reveal metabolic mechanisms of Nitraria sibirica Pall. to salt stress

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Huanyong Li ◽  
Xiaoqian Tang ◽  
Xiuyan Yang ◽  
Huaxin Zhang
Keyword(s):  
Salt Stress ◽  
Amino Acid ◽  
Salt Tolerance ◽  
Metabolic Pathways ◽  
Amino Acid Metabolism ◽  
Acid Metabolism ◽  
Sulfur Metabolism ◽  
Enrichment Analysis ◽  
Extracellular Region ◽  
Nitraria Sibirica

AbstractNitraria sibirica Pall., a typical halophyte that can survive under extreme drought conditions and in saline-alkali environments, exhibits strong salt tolerance and environmental adaptability. Understanding the mechanism of molecular and physiological metabolic response to salt stress of plant will better promote the cultivation and use of halophytes. To explore the mechanism of molecular and physiological metabolic of N. sibirica response to salt stress, two-month-old seedlings were treated with 0, 100, and 400 mM NaCl. The results showed that the differentially expressed genes between 100 and 400 mmol L−1 NaCl and unsalted treatment showed significant enrichment in GO terms such as binding, cell wall, extemal encapsulating structure, extracellular region and nucleotide binding. KEGG enrichment analysis found that NaCl treatment had a significant effect on the metabolic pathways in N. sibirica leaves, which mainly including plant-pathogen interaction, amino acid metabolism of the beta alanine, arginine, proline and glycine metabolism, carbon metabolism of glycolysis, gluconeogenesis, galactose, starch and sucrose metabolism, plant hormone signal transduction and spliceosome. Metabolomics analysis found that the differential metabolites between the unsalted treatment and the NaCl treatment are mainly amino acids (proline, aspartic acid, methionine, etc.), organic acids (oxaloacetic acid, fumaric acid, nicotinic acid, etc.) and polyhydric alcohols (inositol, ribitol, etc.), etc. KEGG annotation and enrichment analysis showed that 100 mmol L−1 NaCl treatment had a greater effect on the sulfur metabolism, cysteine and methionine metabolism in N. sibirica leaves, while various amino acid metabolism, TCA cycle, photosynthetic carbon fixation and sulfur metabolism and other metabolic pathways have been significantly affected by 400 mmol L−1 NaCl treatment. Correlation analysis of differential genes in transcriptome and differential metabolites in metabolome have found that the genes of AMY2, BAM1, GPAT3, ASP1, CML38 and RPL4 and the metabolites of L-cysteine, proline, 4-aminobutyric acid and oxaloacetate played an important role in N. sibirica salt tolerance control. This is a further improvement of the salt tolerance mechanism of N. sibirica, and it will provide a theoretical basis and technical support for treatment of saline-alkali soil and the cultivation of halophytes.

scholarly journals The Pleiotropic Function of Human Sirtuins as Modulators of Metabolic Pathways and Viral Infections

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 460
Author(s):  
Mohammed Hamed Alqarni ◽  
Ahmed Ibrahim Foudah ◽  
Magdy Mohamed Muharram ◽  
Nikolaos E. Labrou
Keyword(s):  
Metabolic Pathways ◽  
Histone Deacetylases ◽  
Viral Infections ◽  
Cell Physiology ◽  
Functional Roles ◽  
Regulatory Processes ◽  
Complex Functions ◽  
Natural Polyphenol ◽  
Antiviral Targets

Sirtuins (SIRTs) are nicotinamide adenine dinucleotide-dependent histone deacetylases that incorporate complex functions in the mechanisms of cell physiology. Mammals have seven distinct members of the SIRT family (SIRT1-7), which play an important role in a well-maintained network of metabolic pathways that control and adapt the cell to the environment, energy availability and cellular stress. Until recently, very few studies investigated the role of SIRTs in modulating viral infection and progeny. Recent studies have demonstrated that SIRT1 and SIRT2 are promising antiviral targets because of their specific connection to numerous metabolic and regulatory processes affected during infection. In the present review, we summarize some of the recent progress in SIRTs biochemistry and their emerging function as antiviral targets. We also discuss the potential of natural polyphenol-based SIRT modulators to control their functional roles in several diseases including viral infections.

scholarly journals Common issues in the hetero-epitaxial seeding on SiC substrates in the sublimation growth of AlN crystals

2021 ◽  
Vol 127 (8) ◽  
Author(s):  
R. Radhakrishnan Sumathi
Keyword(s):  
Power Electronic ◽  
Etch Pit ◽  
Micro Hole ◽  
Wet Chemical ◽  
The Common ◽  
Common Problems ◽  
Hole Defects ◽  
Sublimation Growth ◽  
Impurity Elements ◽  
Very High

AbstractAluminium nitride (AlN) is a futuristic material for efficient next-generation high-power electronic and optoelectronic applications. Sublimation growth of AlN single crystals with hetero-epitaxial approach using silicon carbide substrates is one of the two prominent approaches emerged, since the pioneering crystal growth work from 1970s. Many groups working on this hetero-epitaxial seeding have abandoned AlN growth altogether due to lot of persistently encountered problems. In this article, we focus on most of the common problems encountered in this process such as macro- and micro-hole defects, cracks, 3D-nucleation, high dislocation density, and incorporation of unintentional impurity elements due to chemical decomposition of the substrate at very high temperatures. Possible ways to successfully solve some of these issues have been discussed. Other few remaining challenges, namely low-angle grain boundaries and deep UV optical absorption, are also presented in the later part of this work. Particular attention has been devoted in this work on the coloration of the crystals with respect to chemical composition. Wet chemical etching gives etch pit density (EPD) values in the order of 105 cm-2 for yellow-coloured samples, while greenish coloration deteriorates the structural properties with EPD values of at least one order more.

scholarly journals Interstrain Variability of Human Vaginal Lactobacillus crispatus for Metabolism of Biogenic Amines and Antimicrobial Activity against Urogenital Pathogens

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4538
Author(s):  
Scarlett Puebla-Barragan ◽  
Emiley Watson ◽  
Charlotte van der Veer ◽  
John A. Chmiel ◽  
Charles Carr ◽  
...  
Keyword(s):  
Biogenic Amines ◽  
Metabolic Pathways ◽  
Vaginal Microbiota ◽  
Comparative Genome Analysis ◽  
Genetic Traits ◽  
Lactobacillus Crispatus ◽  
Vaginal Swabs ◽  
The Common ◽  
Synthesis And Degradation

Lactobacillus crispatus is the dominant species in the vagina of many women. With the potential for strains of this species to be used as a probiotic to help prevent and treat dysbiosis, we investigated isolates from vaginal swabs with Lactobacillus-dominated and a dysbiotic microbiota. A comparative genome analysis led to the identification of metabolic pathways for synthesis and degradation of three major biogenic amines in most strains. However, targeted metabolomic analysis of the production and degradation of biogenic amines showed that certain strains have either the ability to produce or to degrade these compounds. Notably, six strains produced cadaverine, one produced putrescine, and two produced tyramine. These biogenic amines are known to raise vaginal pH, cause malodour, and make the environment more favourable to vaginal pathogens. In vitro experiments confirmed that strains isolated from women with a dysbiotic vaginal microbiota have higher antimicrobial effects against the common urogenital pathogens Escherichia coli and Enterococcus faecium. The results indicate that not all L. crispatus vaginal strains appear suitable for probiotic application and the basis for selection should not be only the overall composition of the vaginal microbiota of the host from which they came, but specific biochemical and genetic traits.

Sign in / Sign up

Export Citation Format

Share Document