Bioinformatics Analysis and Identification of Phytoene Synthase Gene in Microalgae

2021 ◽  
Vol 15 ◽  
Author(s):  
Saeedeh Shaker ◽  
Mohammad Hossein Morowvat ◽  
Younes Ghasemi
Keyword(s):  
Biological Activities ◽  
Average Molecular Weight ◽  
Three Dimensional ◽  
Beta Carotene ◽  
Phytoene Synthase ◽  
Diospyros Kaki ◽  
Long Distance ◽  
Conserved Motif ◽  
A Genome ◽  
Gene Structures

Background: Carotenoids are known as lipophilic secondary metabolites with important biological activities, which are mostly used in the food and pharmaceutical industry. They contribute to the colours of many fruits and flowers. Studies on the biosynthetic pathways of isoprenoids and carotenoids are still scarce, especially in microalgae, and are limited to specific groups Dunaliella spp. In the Chlorophyta taxon of algae, the 2-C-methyl-D-erythritol 4-phosphate/1-deoxy-D-xylulose 5-phosphate (DOXP/MEP) is the synthesis pathway of sterols and carotenoids. Objectives: In this study, we used 12 Psy gene sequences in Dunaliella sp., also Scenedesmus acutus, and Diospyros kaki to investigate a genome-wide search. The results are useful for better identification of carotenoids metabolisms and increasing the production rate of beta-carotene in pharmaceutical, food, and industrial processes. Methods: Phytoene synthase (Psy) from Dunaliella spp. was selected as the first regulatory point in the carotenoids pathway that catalysis the formation of geranylgeranyl pyrophosphate in isoprenoid biosynthesis. Structural, evolutionary, and physics-chemical characteristics were investigated using various bioinformatics tools and computer techniques. Moreover, some recently published patents were also regarded. Results: The maximum length of the conserved motif was 5167 bp for Dunaliella. sp. (DQ463306.1), and the smallest length of the conserved motif was 416 bp belong to D. salina (JQ762451.1). The average molecular weight of species was 41820.53 Da. The theoretical pI of species varied from 4.87 to 9.65, indicating vernation in the acidic nature. Two strains of D. bardawil (U91900.1 and EU328287.1) showed just a long-distance relationship with all other Dunaliella strains. Whilst, D. parva displayed the furthest vicinity with all the studied strains. Conclusion: Our study highlighted the Psy regulatory mechanism as a key factor in the carotenoids pathway to facilitate genetic and metabolic engineering studies. The obtained three-dimensional arrangement of the amino acids revealed the regional structures and folding of the diverse segments of helices, sheets, turns. This information is a key point to unveil the protein's operation mechanism. Besides, we confirmed the suitability of bioinformatic approaches for analysing the gene structures and identifying the new Psy genes in unstudied microalgal strains.

scholarly journals GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data

2019 ◽  
Author(s):  
Oluwatosin Oluwadare ◽  
Max Highsmith ◽  
Jianlin Cheng
Keyword(s):  
Structure Prediction ◽  
Biological Activities ◽  
Genome Structure ◽  
3D Structure ◽  
Three Dimensional ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Reconstruction Methods ◽  
A Genome ◽  
Structure Reconstruction

ABSTRACTAdvances in the study of chromosome conformation capture (3C) technologies, such as Hi-C technique - capable of capturing chromosomal interactions in a genome-wide scale - have led to the development of three-dimensional (3D) chromosome and genome structure reconstruction methods from Hi-C data. The 3D genome structure is important because it plays a role in a variety of important biological activities such as DNA replication, gene regulation, genome interaction, and gene expression. In recent years, numerous Hi-C datasets have been generated, and likewise, a number of genome structure construction algorithms have been developed. However, until now, there has been no freely available repository for 3D chromosome structures. In this work, we outline the construction of a novel Genome Structure Database (GSDB) to create a comprehensive repository that contains 3D structures for Hi-C datasets constructed by a variety of 3D structure reconstruction tools. GSDB contains over 50,000 structures constructed by 12 state-of-the-art chromosome and genome structure prediction methods for publicly used Hi-C datasets with varying resolution. The database is useful for the community to study the function of genome from a 3D perspective. GSDB is accessible at http://sysbio.rnet.missouri.edu/3dgenome/GSDB

scholarly journals Plant-Derived Nano and Microvesicles for Human Health and Therapeutic Potential in Nanomedicine

Pharmaceutics ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 498
Author(s):  
Mariaevelina Alfieri ◽  
Antonietta Leone ◽  
Alfredo Ambrosone
Keyword(s):  
Therapeutic Potential ◽  
Biological Activities ◽  
Plant Biotechnology ◽  
Bioactive Metabolites ◽  
Anticancer Activities ◽  
Long Distance ◽  
In Vivo Models ◽  
Therapeutic Tools

Plants produce different types of nano and micro-sized vesicles. Observed for the first time in the 60s, plant nano and microvesicles (PDVs) and their biological role have been inexplicably under investigated for a long time. Proteomic and metabolomic approaches revealed that PDVs carry numerous proteins with antifungal and antimicrobial activity, as well as bioactive metabolites with high pharmaceutical interest. PDVs have also been shown to be also involved in the intercellular transfer of small non-coding RNAs such as microRNAs, suggesting fascinating mechanisms of long-distance gene regulation and horizontal transfer of regulatory RNAs and inter-kingdom communications. High loading capacity, intrinsic biological activities, biocompatibility, and easy permeabilization in cell compartments make plant-derived vesicles excellent natural or bioengineered nanotools for biomedical applications. Growing evidence indicates that PDVs may exert anti-inflammatory, anti-oxidant, and anticancer activities in different in vitro and in vivo models. In addition, clinical trials are currently in progress to test the effectiveness of plant EVs in reducing insulin resistance and in preventing side effects of chemotherapy treatments. In this review, we concisely introduce PDVs, discuss shortly their most important biological and physiological roles in plants and provide clues on the use and the bioengineering of plant nano and microvesicles to develop innovative therapeutic tools in nanomedicine, able to encompass the current drawbacks in the delivery systems in nutraceutical and pharmaceutical technology. Finally, we predict that the advent of intense research efforts on PDVs may disclose new frontiers in plant biotechnology applied to nanomedicine.

scholarly journals Three-Dimensional Zirconia-Based Scaffolds for Load-Bearing Bone-Regeneration Applications: Prospects and Challenges

Materials ◽  
2021 ◽  
Vol 14 (12) ◽  
pp. 3207
Author(s):  
Kumaresan Sakthiabirami ◽  
Vaiyapuri Soundharrajan ◽  
Jin-Ho Kang ◽  
Yunzhi Peter Yang ◽  
Sang-Won Park
Keyword(s):  
Bone Regeneration ◽  
Biological Activities ◽  
Three Dimensional ◽  
In Vivo Studies ◽  
High Mechanical Strength ◽  
Real World Applications ◽  
3D Fabrication ◽  
Dental Applications

The design of zirconia-based scaffolds using conventional techniques for bone-regeneration applications has been studied extensively. Similar to dental applications, the use of three-dimensional (3D) zirconia-based ceramics for bone tissue engineering (BTE) has recently attracted considerable attention because of their high mechanical strength and biocompatibility. However, techniques to fabricate zirconia-based scaffolds for bone regeneration are in a stage of infancy. Hence, the biological activities of zirconia-based ceramics for bone-regeneration applications have not been fully investigated, in contrast to the well-established calcium phosphate-based ceramics for bone-regeneration applications. This paper outlines recent research developments and challenges concerning numerous three-dimensional (3D) zirconia-based scaffolds and reviews the associated fundamental fabrication techniques, key 3D fabrication developments and practical encounters to identify the optimal 3D fabrication technique for obtaining 3D zirconia-based scaffolds suitable for real-world applications. This review mainly summarized the articles that focused on in vitro and in vivo studies along with the fundamental mechanical characterizations on the 3D zirconia-based scaffolds.

scholarly journals Using Externally Bonded CFRP to Repair a PCCP with Broken Wires under Combined Loads

2019 ◽  
Vol 2019 ◽  
pp. 1-11
Author(s):  
Kejie Zhai ◽  
Hongyuan Fang ◽  
Bing Fu ◽  
Fuming Wang ◽  
Benyue Hu
Keyword(s):  
Prestressed Concrete ◽  
Three Dimensional ◽  
Soil Pressure ◽  
Long Distance ◽  
Stress Strain ◽  
Wire Breakage ◽  
Water Pipelines ◽  
Externally Bonded ◽  
Prestressed Concrete Cylinder Pipe ◽  
Three Dimensional Finite Element

Prestressed concrete cylinder pipe (PCCP) is widely used for long-distance water pipelines throughout the world. However, prestressing wire breakage is the most common form of PCCP damage. For some pipelines that cannot be shut down, a new technique for in-service PCCP repair by externally bonding the pipe with layers of carbon fiber reinforced polymer (CFRP) was proposed. A set of three-dimensional finite element models of the repaired PCCP have been proposed and implemented in the ABAQUS software, which took into account the soil pressure, the weight of the PCCP, the weight of the water, and the hydrostatic pressure. The stress–strain features of the PCCP repaired with CFRP of various thicknesses were analyzed. The stress–strain features of different wire breakage rates for the repaired PCCP were also analyzed. The results showed that the strains and stresses decreased at the springline if the PCCP was repaired with CFRP, which improved the operation of the PCCP. It has been found that the wire breakage rates had a significant effect on the strains and stresses of each PCCP component, but CFRP failed to reach its potential tensile strength when other materials were broken.

The Calculation of Train Slipstreams on Platform of Underground High-Speed Rail Station

2013 ◽  
Vol 842 ◽  
pp. 445-448
Author(s):  
Wei Chao Yang ◽  
Chuan He ◽  
Li Min Peng
Keyword(s):  
High Speed ◽  
Three Dimensional ◽  
Horizontal Distribution ◽  
Wake Flow ◽  
Railway Tunnel ◽  
Long Distance ◽  
Near Wake ◽  
High Speed Rail ◽  
Numerical Work ◽  
Rail Station

This paper describes the results of numerical work to determine the flow structures of the slipstream and wake of a high speed train on platforms of underground rail station using three-dimensional compressible Euler equation. The simulations were carried out on a model of a simplified three-coach train and typical cross-section of Chinese high-speed railway tunnel. A number of issues were observed: change process of slipstreams, longitudinal and horizontal distribution characteristics of train wind. Localized velocity peaks were obtained near the nose of the train and in the near wake region. Maximum and minimum velocity values were also noticed near to the nose rear tip. These structures extended for a long distance behind the train in the far wake flow. The slipstream in platform shows the typical three-dimensional characteristics and the velocity is about 4 m/s at 6 m away from the edge of platform.

Assessment of α-calcium sulfate hemihydrate/nanocellulose composite bone graft material for bone healing in a rabbit femoral condyle model

2021 ◽  
Vol 11 (9) ◽  
pp. 1497-1504
Author(s):  
Jinlong Liu ◽  
Yicai Zhang ◽  
Lin Qiu ◽  
Yujuan Zhang ◽  
Bin Gao
Keyword(s):  
Bone Graft ◽  
Calcium Sulfate ◽  
Biological Activities ◽  
Femoral Condyle ◽  
Three Dimensional ◽  
Graft Material ◽  
Bone Graft Material ◽  
Calcium Sulfate Hemihydrate ◽  
Composite Bone

The material properties of nanocellulose (NC) can effectively enhance the structural stability of composite materials. However, the research related to NC/α-calcium sulfate hemihydrate (CSH) composites is largely lacking. In this paper, we explore the combination of these two materials and determine their elaborate biological activities in vivo. Using α-CSH as the matrix, the composite bone graft materials were produced according to different proportions of NC. Then the mechanical strength of the composite bone graft was measured, and the results were analyzed by X-ray diffraction and scanning electron microscopy (SEM). To conduct the material in vivo evaluation, 0% (CN0) and 0.75% (CN0.75) NC/α-CSH composite bone graft materials were implanted into a femoral condyle defect model. The results indicated that NC could significantly enhance the mechanical properties of α-CSH. The SEM analysis indicated that the NC shuttled between the crystal gaps and formed a three-dimensional network structure, which was firmly combined with the crystal structure. Meanwhile, the CN0.75 scaffold remained at 12 weeks postoperation, which provided a long-term framework for new bone formation. Overall, our findings demonstrate that, with a 0.75% NC/α-CSH composite demonstrating good potential as a bone graft material for clinical bone grafting.

scholarly journals Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation

2018 ◽  
Vol 4 (12) ◽  
pp. eaav8550 ◽  
Author(s):  
Suhn K. Rhie ◽  
Shannon Schreiner ◽  
Heather Witt ◽  
Chris Armoskus ◽  
Fides D. Lay ◽  
...  
Keyword(s):  
Cell Model ◽  
Expression Profiles ◽  
Neuronal Cells ◽  
Three Dimensional ◽  
Gene Expression Profiles ◽  
Regulatory Elements ◽  
A Genome ◽  
Wide Scale ◽  
Cell Model System ◽  
Distal Regulatory Elements

As part of PsychENCODE, we developed a three-dimensional (3D) epigenomic map of primary cultured neuronal cells derived from olfactory neuroepithelium (CNON). We mapped topologically associating domains and high-resolution chromatin interactions using Hi-C and identified regulatory elements using chromatin immunoprecipitation and nucleosome positioning assays. Using epigenomic datasets from biopsies of 63 living individuals, we found that epigenetic marks at distal regulatory elements are more variable than marks at proximal regulatory elements. By integrating genotype and metadata, we identified enhancers that have different levels corresponding to differences in genetic variation, gender, smoking, and schizophrenia. Motif searches revealed that many CNON enhancers are bound by neuronal-related transcription factors. Last, we combined 3D epigenomic maps and gene expression profiles to predict enhancer-target gene interactions on a genome-wide scale. This study not only provides a framework for understanding individual epigenetic variation using a primary cell model system but also contributes valuable data resources for epigenomic studies of neuronal epithelium.

scholarly journals Systematic functional characterization of antisense eRNA of protocadherin α composite enhancer

2021 ◽  
Vol 35 (19-20) ◽  
pp. 1383-1394
Author(s):  
Yuxiao Zhou ◽  
Siyuan Xu ◽  
Mo Zhang ◽  
Qiang Wu
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Single Cells ◽  
Functional Characterization ◽  
Three Dimensional ◽  
Elongation Factor ◽  
Locked Nucleic Acid ◽  
Loop Formation ◽  
Long Distance ◽  
Enhancer Region

Enhancers generate bidirectional noncoding enhancer RNAs (eRNAs) that may regulate gene expression. At present, the eRNA function remains enigmatic. Here, we report a 5′ capped antisense eRNA PEARL (Pcdh eRNA associated with R-loop formation) that is transcribed from the protocadherin (Pcdh) α HS5-1 enhancer region. Through loss- and gain-of-function experiments with CRISPR/Cas9 DNA fragment editing, CRISPRi, and CRISPRa, as well as locked nucleic acid strategies, in conjunction with ChIRP, MeDIP, DRIP, QHR-4C, and HiChIP experiments, we found that PEARL regulates Pcdhα gene expression by forming local RNA–DNA duplexes (R-loops) in situ within the HS5-1 enhancer region to promote long-distance chromatin interactions between distal enhancers and target promoters. In particular, increased levels of eRNA PEARL via perturbing transcription elongation factor SPT6 lead to strengthened local three-dimensional chromatin organization within the Pcdh superTAD. These findings have important implications regarding molecular mechanisms by which the HS5-1 enhancer regulates stochastic Pcdhα promoter choice in single cells in the brain.

scholarly journals Podophyllotoxin and Quercetin in Silico Derivatives Docking Analysis with Cyclooxygenase-2 and Aminopeptidase-N

2021 ◽  
Author(s):  
A.E. Manukyan ◽  
A.A. Hovhannisyan
Keyword(s):  
In Silico ◽  
Biological Activities ◽  
Three Dimensional ◽  
Aminopeptidase N ◽  
Docking Analysis ◽  
Quercetin Derivatives ◽  
Pubchem Database ◽  
A Cell ◽  
Cox 2 ◽  
High Level

ABSTRACTThe cyclooxygenase (COX) enzymes are tumor markers, the inhibition of which can be used in the prevention and therapy of carcinogenesis. It was found that COX-2 IS considered as targets for tumor inhibition. Aminopeptidase N (APN) is a type II membrane-bound metalloprotease associated with cancer, being identified as a cell marker on the surface of malignant myeloid cells and reached a high level of expression in progressive tumors. In anticancer therapy, plant compounds are considered that can inhibit their activity. Modeling of the COX-2 and APN enzymes was carried out on the basis of molecular models of three-dimensional structures from the PDB database [PDB ID: 5f19, 4fyq] RCSB. For docking analysis, 3D ligand models were created using MarvinSketch based on the PubChem database [CID: 5280343, 5281654]. In silico experiments, for the first time, revealed the possible interaction and inhibition of COX-2 and APN by quercetin and quercetin derivatives. Aspirin and Marimastat were taken to compare the results. Possible biological activities and possible side effects of the ligands have been identified.

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