scholarly journals Dynamical Modeling of the Core Gene Network Controlling Transition to Flowering in Pisum sativum

2021 ◽  
Vol 12 ◽  
Author(s):  
Polina Pavlinova ◽  
Maria G. Samsonova ◽  
Vitaly V. Gursky
Keyword(s):  
Pisum Sativum ◽  
Network Architecture ◽  
Gene Network ◽  
Alternative Hypothesis ◽  
Core Gene ◽  
Regulation Scheme ◽  
In The Wild ◽  
Flowering Initiation ◽  
Growing Conditions ◽  
Transition To Flowering

Transition to flowering is an important stage of plant development. Many regulatory modules that control floral transition are conservative across plants. This process is best studied for the model plant Arabidopsis thaliana. The homologues of Arabidopsis genes responsible for the flowering initiation in legumes have been identified, and available data on their expression provide a good basis for gene network modeling. In this study, we developed several dynamical models of a gene network controlling transition to flowering in pea (Pisum sativum) using two different approaches. We used differential equations for modeling a previously proposed gene regulation scheme of floral initiation in pea and tested possible alternative hypothesis about some regulations. As the second approach, we applied neural networks to infer interactions between genes in the network directly from gene expression data. All models were verified on previously published experimental data on the dynamic expression of the main genes in the wild type and in three mutant genotypes. Based on modeling results, we made conclusions about the functionality of the previously proposed interactions in the gene network and about the influence of different growing conditions on the network architecture. It was shown that regulation of the PIM, FTa1, and FTc genes in pea does not correspond to the previously proposed hypotheses. The modeling suggests that short- and long-day growing conditions are characterized by different gene network architectures. Overall, the results obtained can be used to plan new experiments and create more accurate models to study the flowering initiation in pea and, in a broader context, in legumes.

scholarly journals Evolution of a Core Gene Network for Skeletogenesis in Chordates

PLoS Genetics ◽  
2008 ◽  
Vol 4 (3) ◽  
pp. e1000025 ◽  
Author(s):  
Jochen Hecht ◽  
Sigmar Stricker ◽  
Ulrike Wiecha ◽  
Asita Stiege ◽  
Georgia Panopoulou ◽  
...  
Keyword(s):  
Gene Network ◽  
Core Gene

scholarly journals STANDARDIZATION OF HYDROPONIC AND WILD GROWING TEUCRIUM POLIUM L. BY HPLC

2019 ◽  
Vol 3 (11) ◽  
Author(s):  
Galstyan H. M ◽  
Dumanyan K. H ◽  
Tsaturyan A. O ◽  
Gukasyan N. H ◽  
Engibaryan A. A ◽  
...  
Keyword(s):  
Acid Anhydride ◽  
The Past ◽  
Phenylpropanoid Glycosides ◽  
In The Wild ◽  
Teucrium Polium ◽  
Water Fractions ◽  
Teucrium Polium L ◽  
Growing Conditions ◽  
Chloroform Methanol ◽  
Solution Volume

It was approved that flavonoids (luteoline, apigenin) and phenylpropanoid glycosides verbascoside best separation was implemented by using UM detector and isocratic isolation regime. Depending on the growing conditions main influencing substance quantities fluctuate: in the wild growing plants were synthesized nearly 2 times more than in hydroponic growing plants. For the study were obtained 500 alcoholic extracts from hydroponic and wild growing T. polium. The studied samples before analysis were developed three-chloral-acetic-acid anhydride and centrifuged by 10 minutes 12000 rev/m speeds. The solution volume of each injected analysis was 10 mkl. Then some amount of standard verbascoside, luteolin and apigenin samples were solved in 1ml ethyl alcohol and were filled into the special test tubes for analysis. By T. polium chloroform-methanol and tower chromatography water fractions teupolizoid, verbascoside and poliumozid phenylpropanoid glycosides were separated which Rf were equal to 0.25, 0.5, 0.37 in our researches in the past. These compounds composition was proved by complex spectroscopic methods. They had close structure to each other and verbascoside enclosed peaks in HPLC were supposed that belong to poliumozid and teupoliozid and also was brought the above mentioned compounds quantities by calculating chromatography data. Keywords: Teucrium polium L., wild and hydroponic, HPLC, standardization, verbascoside, apigenine, luteolin.

scholarly journals FDN: Feature Decoupling Network for Head Pose Estimation

2020 ◽  
Vol 34 (07) ◽  
pp. 12789-12796
Author(s):  
Hao Zhang ◽  
Mengmeng Wang ◽  
Yong Liu ◽  
Yi Yuan
Keyword(s):  
Pose Estimation ◽  
Network Architecture ◽  
Latent Variable ◽  
Spatial Information ◽  
Head Pose Estimation ◽  
Depth Information ◽  
Head Pose ◽  
Large Head ◽  
In The Wild ◽  
Rgb Image

Head pose estimation from RGB images without depth information is a challenging task due to the loss of spatial information as well as large head pose variations in the wild. The performance of existing landmark-free methods remains unsatisfactory as the quality of estimated pose is inferior. In this paper, we propose a novel three-branch network architecture, termed as Feature Decoupling Network (FDN), a more powerful architecture for landmark-free head pose estimation from a single RGB image. In FDN, we first propose a feature decoupling (FD) module to explicitly learn the discriminative features for each pose angle by adaptively recalibrating its channel-wise responses. Besides, we introduce a cross-category center (CCC) loss to constrain the distribution of the latent variable subspaces and thus we can obtain more compact and distinct subspaces. Extensive experiments on both in-the-wild and controlled environment datasets demonstrate that the proposed method outperforms other state-of-the-art methods based on a single RGB image and behaves on par with approaches based on multimodal input resources.

Effect of Postplant Tillage and Crop Density on Broadleaf Weed Control in Dry Pea (Pisum sativum) and Lentil (Lens culinaris)

1995 ◽  
Vol 9 (1) ◽  
pp. 99-106 ◽  
Author(s):  
Chris M. Boerboom ◽  
Frank L. Young
Keyword(s):  
Pisum Sativum ◽  
Weed Control ◽  
Crop Yield ◽  
Weed Management ◽  
Lens Culinaris ◽  
Crop Density ◽  
Growing Conditions ◽  
One Year ◽  
Favorable Conditions ◽  
Crop Competition

Increased crop densities and postplant tillage were evaluated as nonchemical methods to supplement metribuzin for improved broadleaf weed control in dry pea and lentil. The effects of 50, 100, and 150% of recommended 220 kg/ha pea and 67 kg/ha lentil seeding rates and two dates of rotary hoeing and harrowing on pea, lentil, and broadleaf weeds were studied with and without metribuzin for two years. Under favorable growing conditions, crop competition gave 72 and 99% weed control in pea and 33 and 70% weed control in lentil with the 50 and 150% seeding rates. Under less favorable conditions, control was 21 to 39% with the low and high pea and lentil seeding rates. At recommended seeding rates, metribuzin gave greater than 90% control in either crop or year. Postplant tillage 12 to 27 d after planting slightly reduced crop densities in three tillage treatments in one year, but not the second. Postplant tillage did not affect crop yield or improve weed control. In all studies, pea was similar to or more competitive than lentil in suppressing broadleaf weeds. Because neither non-chemical practice significantly improves weed control, changes are not recommended for weed management in pea and lentil.

scholarly journals Gene network in pulmonary tuberculosis based on bioinformatic analysis

2020 ◽  
Author(s):  
Lili Li ◽  
Jian Lv ◽  
Yuan He ◽  
Zhihua Wang
Keyword(s):  
Pulmonary Tuberculosis ◽  
Chemokine Receptors ◽  
Gene Network ◽  
Kegg Pathway ◽  
Bioinformatic Analysis ◽  
Core Gene ◽  
Ppi Network ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Causal Genes

Abstract Background: Pulmonary tuberculosis (PTB) is one of the serious infectious diseases worldwide; however, the gene network involved in the host response remain largely unclear. Methods: This study integrated two cohorts profile datasets GSE34608 and GSE83456 to elucidate the potential gene network and signaling pathways in PTB. Differentially expressed genes (DEGs) were obtained for Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis using Metascape database. Protein-Protein Interaction (PPI) network of DEGs was constructed by the online database the Search Tool for the Retrieval of Interacting Genes (STRING). Modules were identified by the plug-in APP Molecular Complex Detection (MCODE) in Cytoscape. GO and KEGG pathway of Module 1 were further analyzed by STRING. Hub genes were selected for further expression validation in dataset GSE19439. The gene expression level was also investigated in the dataset GSE31348 to display the change pattern during the PTB treatment. Results: Totally, 180 shared DEGs were identified from two datasets. Gene function and KEGG pathway enrichment revealed that DEGs mainly enriched in defense response to other organism, response to bacterium, myeloid leukocyte activation, cytokine production, etc. Seven modules were clustered based on PPI network. Module 1 contained 35 genes related to cytokine associated functions, among which 14 genes, including chemokine receptors, interferon-induced proteins and Toll-like receptors, were identified as hub genes. Expression levels of the hub genes were validated with a third dataset GSE19439. The signature of this core gene network showed significant response to Mycobacterium tuberculosis (Mtb) infection, and correlated with the gene network pattern during anti-PTB therapy. Conclusions: Our study unveils the coordination of causal genes during PTB infection, and provides a promising gene panel for PTB diagnosis. As major regulators of the host immune response to Mtb infection, the 14 hub genes are also potential molecular targets for developing PTB drugs.

scholarly journals Gene network modeling via TopNet reveals robust epistatic interactions between functionally diverse tumor critical mediator genes

2020 ◽  
Author(s):  
Helene R. McMurray ◽  
Aslihan Ambeskovic ◽  
Laurel A. Newman ◽  
Jordan Aldersley ◽  
Vijaya Balakrishnan ◽  
...  
Keyword(s):  
Network Architecture ◽  
Gene Network ◽  
Cell Transformation ◽  
Network Modeling ◽  
Malignant Cell ◽  
Gene Interactions ◽  
Novel Approach ◽  
Genetic Perturbations ◽  
Perturbation Data ◽  
Cancer Intervention

AbstractMalignant cell transformation and the underlying genomic scale reprogramming of gene expression require cooperation of multiple oncogenic mutations. Notably, this cooperation is reflected in the synergistic regulation of downstream genes, so-called cooperation response genes (CRGs). CRGs impact diverse hallmark features of cancer cells and are not known to be functionally connected. Yet, they act as critical mediators of the cancer phenotype at an unexpectedly high frequency of >50%, as indicated by genetic perturbations. Here we demonstrate that CRGs function within a network of strong genetic interdependencies that are critical to the robustness of the malignant state. Our approach, termed TopNet, utilizes attractor-based ternary network modeling that takes the novel approach of incorporating uncertainty in the underlying gene perturbation data and is capable of identifying non-linear gene interactions. TopNet reveals topological gene network architecture that effectively predicts previously unknown, functionally relevant epistatic gene interactions, and thus, among a broad range of applications, has utility for identification of non-mutant targets for cancer intervention.

Cultivating the increasingly popular medicinal plant, goldenseal: Review and update

2001 ◽  
Vol 16 (3) ◽  
pp. 131-140 ◽  
Author(s):  
Adrianne Sinclair ◽  
Paul M. Catling
Keyword(s):  
Organic Matter ◽  
Sandy Loam ◽  
Crop Improvement ◽  
Natural Populations ◽  
In The Wild ◽  
Northern Portion ◽  
Natural Range ◽  
Growing Conditions ◽  
Requirements Development ◽  
Rotation Crop

AbstractInterest in the cultivation of goldenseal is increasing and this may have benefits for agriculture, human health, and conservation. To enable a better understanding of growing conditions, cultivation methods reported in the literature were reviewed, 21 natural goldenseal populations in the northern portion of its natural range in North America were described and analyzed in terms of population size and health, and 15 successful growers were interviewed on requirements for optimal cultivation. Growing conditions in the wild were compared to those reported in the cultivation literature. Summary of data from natural populations suggests goldenseal grows best in mixed hardwood forests, under 60–65% shade, in moist sandy loam soils high in organic matter, with pH 5.7 to 6.3. Similarly, review of the literature suggests that goldenseal grows best in moist, well-drained loams high in organic matter, with pH 5.5 to 6.5. Reported shade requirements vary but 47–80% shade is considered optimal. Growing conditions reported by growers were also consistent with the cultivation literature and similar to conditions of wild populations. Although optimal growing conditions are similar to those for many crops, goldenseal is relatively robust and can grow well in a variety of conditions including wet, predominantly sandy or clay soils with pH as low as 4.8 and as high as 7.8. Cultivation can utilize a ginseng crop infrastructure and goldenseal has been recommended as a rotation crop for ginseng. Commercial production of goldenseal is potentially advantageous because (1) it is an environmentally friendly crop; (2) it has been grown successfully far outside its natural range, is easy to grow, and is considered potentially profitable; and (3) it is relatively inexpensive, having low energy, land area, and fertilization requirements. Development of a sustainable crop may contribute to the protection of native wild germplasm, which can provide valuable material for crop improvement.

scholarly journals Kriteriji kvalitete biljnog materijala i eteričnog ulja primorskog smilja (Helichrysum italicum (Roth.) G. Don)

2019 ◽  
Vol 7 (1) ◽  
pp. 425-431
Author(s):  
Martina Peršić ◽  
Karla Leko ◽  
Slavica Dudaš
Keyword(s):  
Chemical Composition ◽  
Essential Oil ◽  
Plant Material ◽  
Folk Medicine ◽  
Market Price ◽  
Quality Criteria ◽  
In The Wild ◽  
Ancient Times ◽  
Growing Conditions

Immortelle (Helichrysum italicum) is a xerophytic plant species naturally present in the wild population of Mediterranean on karst and dry terrains. Since ancient times, the immortelle has been known as a “non-vein plant” and is highly valued due to its wide application in folk medicine. Antimicrobial, antiviral, anti-inflammatory, antioxidative, regenerative, insecticidal and repellent properties of essential oil and hydrolates are a frequent subject of recent research. The chemical composition of the essential oil and characteristics of plant material have a direct effect on market price. This research was conducted by a survey of producers and buyers of immortelle plant material and essential oil with the aim to gather information on the quality criteria of plant material and essential oil. The collected data showed that the basic criteria for quality determination of plant material are controlled growing conditions and the main parameters affecting the price of the essential oil are chemical composition, i.e. the content and ratio of α-pinene and neryl acetate.

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