scholarly journals Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data

2001 ◽  
Vol 29 (1) ◽  
pp. 80-81 ◽  
Author(s):  
C. A. Ball
Keyword(s):  
Gene Expression ◽  
Functional Analysis ◽  
Analysis Data ◽  
Saccharomyces Genome Database ◽  
Genome Database ◽  
Functional Analysis Data

Using Real-Time Recording to Enhance the Analysis of Within-Session Functional Analysis Data

2001 ◽  
Vol 25 (1) ◽  
pp. 79-93 ◽  
Author(s):  
John T. Rapp ◽  
James E. Carr ◽  
Raymond G. Miltenberger ◽  
Claudia L. Dozier ◽  
Karen K. Kellum
Keyword(s):  
Functional Analysis ◽  
Real Time ◽  
Analysis Data ◽  
Functional Analysis Data

scholarly journals TOWARD THE DEVELOPMENT OF STRUCTURED CRITERIA FOR INTERPRETATION OF FUNCTIONAL ANALYSIS DATA

1997 ◽  
Vol 30 (2) ◽  
pp. 313-326 ◽  
Author(s):  
Louis P. Hagopian ◽  
Wayne W. Fisher ◽  
Rachel H. Thompson ◽  
Jamie Owen-DeSchryver ◽  
Brian A. Iwata ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Analysis Data ◽  
Functional Analysis Data

scholarly journals Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Hui Li ◽  
Xingyu Yang ◽  
Yue Zhang ◽  
Zhiyan Gao ◽  
Yuting Liang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plant Species ◽  
Aquatic Plant ◽  
Molecular Breeding ◽  
Nelumbo Nucifera ◽  
Sequence Analyses ◽  
Genome Database ◽  
Future Studies ◽  
Sacred Lotus ◽  
Coexpression Networks

AbstractSacred lotus (Nelumbo nucifera, or lotus) is one of the most widely grown aquatic plant species with important uses, such as in water gardening and in vegetable and herbal medicine. A public genomic database of lotus would facilitate studies of lotus and other aquatic plant species. Here, we constructed an integrative database: the Nelumbo Genome Database (NGD, http://nelumbo.biocloud.net). This database is a collection of the most updated lotus genome assembly and contains information on both gene expression in different tissues and coexpression networks. In the NGD, we also integrated genetic variants and key traits from our 62 newly sequenced lotus cultivars and 26 previously reported cultivars, which are valuable for lotus germplasm studies. As applications including BLAST, BLAT, Primer, Annotation Search, Variant and Trait Search are deployed, users can perform sequence analyses and gene searches via the NGD. Overall, the valuable genomic resources provided in the NGD will facilitate future studies on population genetics and molecular breeding of lotus.

scholarly journals Mitogenome Analysis of Four Lamiinae Species (Coleoptera: Cerambycidae) and Gene Expression Responses by Monochamus alternatus When Infected with the Parasitic Nematode, Bursaphelenchus mucronatus

Insects ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 453
Author(s):  
Zi-Yi Zhang ◽  
Jia-Yin Guan ◽  
Yu-Rou Cao ◽  
Xin-Yi Dai ◽  
Kenneth B. Storey ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phylogenetic Trees ◽  
Mitochondrial Gene ◽  
Mitochondrial Protein ◽  
Pine Wilt Disease ◽  
Bursaphelenchus Xylophilus ◽  
Monochamus Alternatus ◽  
Genome Database ◽  
Protein Coding ◽  
Nd5 Gene

We determined the mitochondrial gene sequence of Monochamus alternatus and three other mitogenomes of Lamiinae (Insect: Coleoptera: Cerambycidae) belonging to three genera (Aulaconotus, Apriona and Paraglenea) to enrich the mitochondrial genome database of Lamiinae and further explore the phylogenetic relationships within the subfamily. Phylogenetic trees of the Lamiinae were built using the Bayesian inference (BI) and maximum likelihood (ML) methods and the monophyly of Monochamus, Anoplophora, and Batocera genera was supported. Anoplophora chinensis, An. glabripennis and Aristobia reticulator were closely related, suggesting they may also be potential vectors for the transmission of the pine wood pathogenic nematode (Bursaphelenchus xylophilus) in addition to M. alternatus, a well-known vector of pine wilt disease. There is a special symbiotic relationship between M. alternatus and Bursaphelenchus xylophilus. As the native sympatric sibling species of B. xylophilus, B. mucronatus also has a specific relationship that is often overlooked. The analysis of mitochondrial gene expression aimed to explore the effect of B. mucronatus on the energy metabolism of the respiratory chain of M. alternatus adults. Using RT-qPCR, we determined and analyzed the expression of eight mitochondrial protein-coding genes (COI, COII, COIII, ND1, ND4, ND5, ATP6, and Cty b) between M. alternatus infected by B. mucronatus and M. alternatus without the nematode. Expression of all the eight mitochondrial genes were up-regulated, particularly the ND4 and ND5 gene, which were up-regulated by 4–5-fold (p < 0.01). Since longicorn beetles have immune responses to nematodes, we believe that their relationship should not be viewed as symbiotic, but classed as parasitic.

scholarly journals 137 Dietary Supplementations of Ethanolamine and Serine Enhance Docosahexaenoic Acid Deposition in Eggs of Laying Hens

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 107-108
Author(s):  
Andrew D Magnuson ◽  
Xingen Lei
Keyword(s):  
Gene Expression ◽  
Docosahexaenoic Acid ◽  
Laying Hens ◽  
Total Phospholipid ◽  
Choline Chloride ◽  
Basal Diet ◽  
Egg Yolk ◽  
Analysis Data ◽  
Mrna Levels ◽  
Dha Enrichment

Abstract Enrichment of docosahexaenoic-acid (DHA) into eggs of laying-hens may be limited by the availability phospholipids as a deposition sink. The present study was to determine if dietary supplementations of phospholipid-component molecules or synthesis-enhancers: choline, serine, and ethanolamine could elevate phospholipid and DHA enrichment in the eggs and tissues of hens. A total of 50-White-Leghorn-Shavers (42-wk old) were individually caged and divided into 5 groups (n = 10/group). The 5 groups of hens were fed the following diets for 3 wk: Diet-1 = a corn soybean-meal basal-diet, Diet-2 = Diet-1 + 4%-microalgae (Aurantiochytrium, Heliae, Gibert, AZ, 1.81 g-DHA/kg) + choline-chloride (26.3 g/kg diet, 60% purity, DSM-Co., Basel, Switzerland), Diet-3 = Diet-2 + 1.41% of L-serine (100% purity, Ajinomoto-Co., Inc., Kawasaki, Japan), Diet-4 = Diet-2 + 100 mg of ethanolamine/kg (99% purity, Sigma-Aldirch-Co., St Loius, MO), and Diet-5 = Diet-3 + 100 mg of ethanolamine/kg. At the end of study, eggs, liver, ovary, and adipose samples were collected from 6 hens/group for biochemical analysis. Data were analyzed by one-way ANOVA. Compared with Diet-1, Diet-2 enhanced (P &lt; 0.05) DHA concentrations in egg yolk and liver by 213 mg/egg and 2.98 mg/g tissue, respectively, but decreased (P &lt; 0.05) total phospholipid-concentrations of yolk and liver by 50%, and hepatic-mRNA levels of elongases-2/5 and desaturases-4/6 by 25–50%. Compared with Diet-2, Diet-5 enhanced (P &lt; 0.05) DHA (by 20%) and phospholipid (by 40%) concentrations in the egg yolk, and upregulated (P &lt; 0.05) lipid-metabolism genes involved in the citicoline (CDP, up-to-3-fold) and CDP-ethanolamine (up-to-2.5-fold) pathways in the liver and ovary-tissue. In comparison, Diets-3 and 4 resulted in only 3–11% higher (P &lt; 0.05) DHA-concentrations in the liver over Diet-2. In conclusion, feeding hens a high DHA and choline diet enriched DHA in the egg yolk and down-regulated lipogenesis-gene-expression in the tissues. Supplementing the diet with extra-serine and ethanolamine further-enhanced the DHA enrichment in the egg yolk and restored the high DHA-mediated changes in the gene-expression. (Supported in part by DOE-MAGIC-grant DE-EE0007091, USDA-grant 2019-69012-29905, and Cornell-University-Hatch-grants NYC-127419/127302).

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