scholarly journals BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 4
Author(s):  
Caroline Gaud ◽  
Bebiana C. Sousa ◽  
An Nguyen ◽  
Maria Fedorova ◽  
Zhixu Ni ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Biological Sample ◽  
Biosynthetic Pathways ◽  
Single Experiment ◽  
Web Based ◽  
Lipid Molecular Species ◽  
Large Numbers ◽  
Mammalian Tissues ◽  
Biological Differences ◽  
Multiple Categories

Lipidomics increasingly describes the quantification using mass spectrometry of all lipids present in a biological sample.  As the power of lipidomics protocols increase, thousands of lipid molecular species from multiple categories can now be profiled in a single experiment.  Observed changes due to biological differences often encompass large numbers of structurally-related lipids, with these being regulated by enzymes from well-known metabolic pathways.  As lipidomics datasets increase in complexity, the interpretation of their results becomes more challenging.  BioPAN addresses this by enabling the researcher to visualise quantitative lipidomics data in the context of known biosynthetic pathways.  BioPAN provides a list of genes, which could be involved in the activation or suppression of enzymes catalysing lipid metabolism in mammalian tissues.

scholarly journals BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 4
Author(s):  
Caroline Gaud ◽  
Bebiana C. Sousa ◽  
An Nguyen ◽  
Maria Fedorova ◽  
Zhixu Ni ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Biological Sample ◽  
Biosynthetic Pathways ◽  
Single Experiment ◽  
Web Based ◽  
Lipid Molecular Species ◽  
Large Numbers ◽  
Mammalian Tissues ◽  
Biological Differences ◽  
Multiple Categories

Lipidomics increasingly describes the quantitation using mass spectrometry of all lipids present in a biological sample.  As the power of lipidomics protocols increase, thousands of lipid molecular species from multiple categories can now be profiled in a single experiment.  Observed changes due to biological differences often encompass large numbers of structurally-related lipids, with these being regulated by enzymes from well-known metabolic pathways.  As lipidomics datasets increase in complexity, the interpretation of their results becomes more challenging.  BioPAN addresses this by enabling the researcher to visualise quantitative lipidomics data in the context of known biosynthetic pathways.  BioPAN provides a list of genes, which could be involved in the activation or suppression of enzymes catalysing lipid metabolism in mammalian tissues.

scholarly journals Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts

2019 ◽  
Author(s):  
Sergio A Muñoz-Gómez ◽  
Keira Durnin ◽  
Laura Eme ◽  
Christopher Paight ◽  
Christopher E Lane ◽  
...  
Keyword(s):  
Life Style ◽  
Metabolic Pathways ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Biosynthetic Pathways ◽  
History Of ◽  
Sea Squirts ◽  
Shed Light ◽  
Apicoplast Genome

Abstract A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to (1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, (2) search for the apicoplast genome of Nephromyces, and (3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the non-photosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.

scholarly journals Carotenoid Profiling of a Red Seaweed Pyropia yezoensis: Insights into Biosynthetic Pathways in the Order Bangiales

Marine Drugs ◽  
2018 ◽  
Vol 16 (11) ◽  
pp. 426 ◽  
Author(s):  
Jiro Koizumi ◽  
Naoki Takatani ◽  
Noritoki Kobayashi ◽  
Koji Mikami ◽  
Kazuo Miyashita ◽  
...  
Keyword(s):  
1H Nmr ◽  
Metabolic Pathways ◽  
Pyropia Yezoensis ◽  
Biosynthetic Pathways ◽  
Red Seaweed ◽  
Red Seaweeds ◽  
Natural Pigments ◽  
Photosynthetic Organisms ◽  
Metabolic Products ◽  
Β Carotene

Carotenoids are natural pigments that contribute to light harvesting and photo-protection in photosynthetic organisms. In this study, we analyzed the carotenoid profiles, including mono-hydroxy and epoxy-carotenoids, in the economically valuable red seaweed Pyropia yezoensis, to clarify the detailed biosynthetic and metabolic pathways in the order Bangiales. P. yezoensis contained lutein, zeaxanthin, α-carotene, and β-carotene, as major carotenoids in both the thallus and conchocelis stages. Monohydroxy intermediate carotenoids for the synthesis of lutein with an ε-ring from α-carotene, α-cryptoxanthin (β,ε-caroten-3’-ol), and zeinoxanthin (β,ε-caroten-3-ol) were identified. In addition, β-cryptoxanthin, an intermediate in zeaxanthin synthesis from β-carotene, was also detected. We also identified lutein-5,6-epoxide and antheraxanthin, which are metabolic products of epoxy conversion from lutein and zeaxanthin, respectively, by LC-MS and 1H-NMR. This is the first report of monohydroxy-carotenoids with an ε-ring and 5,6-epoxy-carotenoids in Bangiales. These results provide new insights into the biosynthetic and metabolic pathways of carotenoids in red seaweeds.

The morphology and development of Drosophila eye

Development ◽  
1967 ◽  
Vol 17 (3) ◽  
pp. 491-499
Author(s):  
E. W. Hanly ◽  
C. William Fuller ◽  
M. S. Millam Stanley
Keyword(s):  
Drosophila Melanogaster ◽  
Metabolic Pathways ◽  
Biosynthetic Pathways ◽  
Wild Type ◽  
Specific Enzyme ◽  
Type D ◽  
Red Color ◽  
Drosophila Eye ◽  
The Subject

The development of pigment in the eye of Drosophila melanogaster and other insects has been the subject of many studies and much controversy. It has been established that the red color of eyes of wild-type D. melanogaster is due to the presence of two classes of pigments, ommochromes and pteridines (Ziegler, 1961). The relationships among the various members of each class are still obscure; the biosynthetic pathways are yet to be elucidated. No specific enzyme involved in the synthesis of any member of either group has been isolated or characterized. It has been suggested, however (Hadorn, 1955), that these metabolic pathways may involve several organs, including the eye, but that the final deposition and conversion occur only in the eye. The recent development of a satisfactory technique for the culture of Drosophila organs (Schneider, 1964) has made possible the study of pigment development in the isolated eye and in eyes associated with selected organs.

scholarly journals Basic astronomy as part of a general higher education in the developing world

2006 ◽  
Vol 2 (SPS5) ◽  
pp. 257-262
Author(s):  
John Baruch ◽  
Dan Hedges ◽  
James Machell ◽  
K. Norris ◽  
Chris Tallon
Keyword(s):  
General Education ◽  
Developing World ◽  
Current System ◽  
Education Programme ◽  
The Internet ◽  
Web Based ◽  
Astronomy Education ◽  
Large Numbers ◽  
Robotic Telescopes ◽  
Robotic Telescope

AbstractThis paper describes a new initiative in support of the aim of Commission 46 of the IAU to develop and improve astronomy education at all levels throughout the world. This paper discusses the ideal specification of a facility to support basic astronomy within education programmes which are delivered to students who have access to the Internet. The available robotic telescopes are discussed against this specification and it is argued that the Bradford Robotic Telescope, uniquely, can support many thousands of users in the area of basic astronomy education, and the resource is free.Access to the Internet is growing in the developing world and this is true in education programmes. This paper discusses the serious problems of delivering to large numbers of students a web based astronomy education programme supported by a robotic telescope as part of a general education. It examines the problems of this form of teaching for teachers who have little experience of working with IT and little knowledge of basic astronomy and proposes how such teachers can be supported.The current system (http://www.telescope.org/) delivers astronomy education in the language, culture and traditions of England. The paper discusses the need to extend this to other languages, cultures and traditions, although for trainee teachers and undergraduates, it is argued that the current system provides a unique and valuable resource.

Molecular approaches to the manipulation of carbon allocation in plants

1993 ◽  
Vol 71 (6) ◽  
pp. 765-778 ◽  
Author(s):  
S. D. Blakeley ◽  
D. T. Dennis
Keyword(s):  
Amino Acids ◽  
Fatty Acids ◽  
Metabolic Pathways ◽  
Carbon Allocation ◽  
Genetic Manipulation ◽  
Biosynthetic Pathways ◽  
Molecular Approaches ◽  
Carbon Substrates ◽  
Storage Organs ◽  
Storage Products

In plants, sucrose is the end product of photosynthesis and is converted to a wide variety of storage compounds in tissues such as seeds and tubers. The allocation of carbon from sucrose to the various metabolic pathways leading to these products will determine the quantity of each synthesized in the respective storage organs. If the level of the enzymes involved in the allocation of carbon could be changed by genetic manipulation, it is probable that the relative yields of the various storage products can also be altered. The initial breakdown of sucrose occurs in the cytosol of the cell. Many biosynthetic pathways, however, including those involved in the synthesis of storage products such as fatty acids, starch, and amino acids, occur in the plastid. The distribution of carbon substrates for these processes will be determined, to a large extent, by the flux of carbon through the glycolytic pathways found in both the cytosolic and plastid compartments. This article will discuss the importance and consequences of compartmentation, review the extent of our understanding of glycolysis and other enzymes and pathways regulating carbon allocation, and will speculate on the potential for the genetic manipulation of these pathways. Key words: genetic manipulation, carbon allocation, metabolism, glycolysis.

scholarly journals Structure-mining: screening structure models by automated fitting to the atomic pair distribution function over large numbers of models

2020 ◽  
Vol 76 (3) ◽  
pp. 395-409 ◽  
Author(s):  
Long Yang ◽  
Pavol Juhás ◽  
Maxwell W. Terban ◽  
Matthew G. Tucker ◽  
Simon J. L. Billinge
Keyword(s):  
Distribution Function ◽  
Pair Distribution Function ◽  
Complex Oxide ◽  
Web Based ◽  
New Approach ◽  
Atomic Pair Distribution Function ◽  
Large Numbers ◽  
Traditional Structure ◽  
Atomic Pair ◽  
Atomic Crystal

A new approach is presented to obtain candidate structures from atomic pair distribution function (PDF) data in a highly automated way. It fetches, from web-based structural databases, all the structures meeting the experimenter's search criteria and performs structure refinements on them without human intervention. It supports both X-ray and neutron PDFs. Tests on various material systems show the effectiveness and robustness of the algorithm in finding the correct atomic crystal structure. It works on crystalline and nanocrystalline materials including complex oxide nanoparticles and nanowires, low-symmetry and locally distorted structures, and complicated doped and magnetic materials. This approach could greatly reduce the traditional structure searching work and enable the possibility of high-throughput real-time auto-analysis PDF experiments in the future.

scholarly journals Multiplex Genome Editing in Yeast by CRISPR/Cas9 – A Potent and Agile Tool to Reconstruct Complex Metabolic Pathways

2021 ◽  
Vol 12 ◽  
Author(s):  
Joseph Christian Utomo ◽  
Connor Lorne Hodgins ◽  
Dae-Kyun Ro
Keyword(s):  
Genome Editing ◽  
Metabolic Pathways ◽  
Functional Characterization ◽  
Primary Metabolism ◽  
Biosynthetic Pathways ◽  
Post Translational Modification ◽  
Precise Integration ◽  
Specialized Metabolism ◽  
Specialized Metabolites ◽  
Plant Specialized Metabolism

Numerous important pharmaceuticals and nutraceuticals originate from plant specialized metabolites, most of which are synthesized via complex biosynthetic pathways. The elucidation of these pathways is critical for the applicable uses of these compounds. Although the rapid progress of the omics technology has revolutionized the identification of candidate genes involved in these pathways, the functional characterization of these genes remains a major bottleneck. Baker’s yeast (Saccharomyces cerevisiae) has been used as a microbial platform for characterizing newly discovered metabolic genes in plant specialized metabolism. Using yeast for the investigation of numerous plant enzymes is a streamlined process because of yeast’s efficient transformation, limited endogenous specialized metabolism, partially sharing its primary metabolism with plants, and its capability of post-translational modification. Despite these advantages, reconstructing complex plant biosynthetic pathways in yeast can be time intensive. Since its discovery, CRISPR/Cas9 has greatly stimulated metabolic engineering in yeast. Yeast is a popular system for genome editing due to its efficient homology-directed repair mechanism, which allows precise integration of heterologous genes into its genome. One practical use of CRISPR/Cas9 in yeast is multiplex genome editing aimed at reconstructing complex metabolic pathways. This system has the capability of integrating multiple genes of interest in a single transformation, simplifying the reconstruction of complex pathways. As plant specialized metabolites usually have complex multigene biosynthetic pathways, the multiplex CRISPR/Cas9 system in yeast is suited well for functional genomics research in plant specialized metabolism. Here, we review the most advanced methods to achieve efficient multiplex CRISPR/Cas9 editing in yeast. We will also discuss how this powerful tool has been applied to benefit the study of plant specialized metabolism.

scholarly journals Simulation of Ecological and Evolutionary Interactions of Darwin's Finches—A Multimedia Learning Tool

HortScience ◽  
1997 ◽  
Vol 32 (6) ◽  
pp. 983b-983
Author(s):  
R.D. Quinn
Keyword(s):  
Population Size ◽  
Pilot Project ◽  
Early Summer ◽  
Initial Population ◽  
Introductory Biology ◽  
Web Based ◽  
Darwin's Finches ◽  
Darwin’S Finches ◽  
Large Numbers ◽  
Bill Morphology

Dr. Quinn is one of a team of six biology professors from six different CSU campuses collaborating on this pilot project. EvolvelT is a web-based method for students to learn the fundamentals of natural selection and speciation by simulating natural processes. The simulation will be modeled on the evolution of Darwin's Finches in the Galapagos Islands. Learners will manipulate variables such as initial population size, variability and heritability of bill morphology, and quantity and quality of seeds, and then observe changes with time in population size and bill morphology. The interactive model will allow variables to be changed and simulations to be repeated, producing results that can be graphed and statistically analyzed. The Integrated Technology Strategy (ITS) of the California State University System (CSU) is using the Internet to create new and more flexible learning opportunities. Recently the ITS brought together biologists from several CSU campuses to explore ways to use technology to improve learning in introductory biology laboratories for non-science students. These laboratories were chosen because they affect large numbers of students at all campuses. Development criteria include applicability across the CSU, improvement in learning quality, accessibility to large numbers of students, and measurable success. We selected evolution as a topic for web-based learning because it is a central concept of biology, and it is relatively difficult to teach in conventional introductory biology laboratories. Our development team will work with multimedia design specialists to insure that the web presentation promotes scientifically sound and efficient learning. We are collaborating via e-mail and occasional video conferences and face-to-face meetings. We will work on the actual teaching materials via a web page. The initial prototype will be ready by early summer 1997 and will be tested, modified, and released for beta testing by summer's end.

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