scholarly journals Insights of the Neofusicoccum parvum–Liquidambar styraciflua Interaction and Identification of New Cysteine-Rich Proteins in Both Species

2021 ◽  
Vol 7 (12) ◽  
pp. 1027
Author(s):  
Rebeca Vázquez-Avendaño ◽  
José Benjamín Rodríguez-Haas ◽  
Hugo Velázquez-Delgado ◽  
Greta Hanako Rosas-Saito ◽  
Eric Edmundo Hernández-Domínguez ◽  
...  
Keyword(s):  
In Silico Analysis ◽  
Infection Process ◽  
Liquidambar Styraciflua ◽  
Genomic Databases ◽  
Neofusicoccum Parvum ◽  
Disease Symptoms ◽  
Foliar Tissue ◽  
First Time ◽  
Silico Analysis

Neofusicoccum parvum belongs to the Botryosphaeriaceae family, which contains endophytes and pathogens of woody plants. In this study, we isolated 11 strains from diseased tissue of Liquidambar styraciflua. Testing with Koch’s postulates—followed by a molecular approach—revealed that N. parvum was the most pathogenic strain. We established an in vitro pathosystem (L. styraciflua foliar tissue–N. parvum) in order to characterize the infection process during the first 16 days. New CysRPs were identified for both organisms using public transcriptomic and genomic databases, while mRNA expression of CysRPs was analyzed by RT-qPCR. The results showed that N. parvum caused disease symptoms after 24 h that intensified over time. Through in silico analysis, 5 CysRPs were identified for each organism, revealing that all of the proteins are potentially secreted and novel, including two of N. parvum proteins containing the CFEM domain. Interestingly, the levels of the CysRPs mRNAs change during the interaction. This study reports N. parvum as a pathogen of L. styraciflua for the first time and highlights the potential involvement of CysRPs in both organisms during this interaction.

scholarly journals First molecular insights into the infection process provoked by Neofusicoccum parvum in Liquidambar styraciflua and the identification of new cysteine rich proteins in both organisms

2020 ◽  
Author(s):  
Rebeca Vázquez-Avendaño ◽  
José Benjamín Rodríguez-Haas ◽  
Hugo Velázquez-Delgado ◽  
Greta Hanako Rosas-Saito ◽  
Eric Edmundo Hernández-Domínguez ◽  
...  
Keyword(s):  
Post Infection ◽  
Molecular Mechanisms ◽  
Phylogenetic Analyses ◽  
Leaf Tissue ◽  
Infection Process ◽  
Liquidambar Styraciflua ◽  
Broad Host Range ◽  
Neofusicoccum Parvum ◽  
First Time

Abstract Background Neofusicoccum parvum belongs to Botryosphaeriaceae family that groups endophytic and latent pathogens of woody plants responsible of diseases such as cankers, dieback and blight. Is a widespread pathogen in a broad host range including agricultural, horticultural and forestry plants, therefore is relevant to characterize molecular mechanisms involved in the disease. This work, report for first time a N. parvum as a pathogen of Liquidambar styraciflua. We established an in vitro pathosystem using foliar tissue in order to characterize the infection process through scanning electron microscopy. Because cysteine rich proteins (CysRPs) are well described for their important functions under plant-pathogen interaction, new CysRPs were identified for these organisms, and mRNAs expression of these proteins was analyzed at early times during the interaction.Results Since the first 24 hours post infection, the pathogen caused visible symptoms and the microscopic analysis at 16 days post infection revealed the presence of N. parvum pycnidium immersed in L. styraciflua leaf tissue. For both organisms, two databases with transcriptomic and genomic information were analyzed and new five CysRPs were identified for each organism, the amino acid length varied between 95 and 204 and in silico analysis revealed that all proteins are potentially secreted. The search of conserved domains and phylogenetic analyses bring to light that all proteins are novel including two of N. parvum that present the well-known CFEM domain. RT-qPCR analysis was conducted at 24- and 72-hours post infection and the results showed change levels of CysRPs mRNAs for both the plant and the fungus at early times during the interaction.ConclusionsIt is recognized for first time that N. parvum is a pathogen of L. styraciflua and this work represents an approach to begin to deeply understand the molecular mechanisms involved in this interaction highlighting the potential involvement of CysRPs of both organism during this biotic stress.

scholarly journals First molecular insights into the infection process provoked by Neofusicoccum parvum in Liquidambar styraciflua and the identification of new cysteine-rich proteins in both organisms

2020 ◽  
Author(s):  
Rebeca Vázquez-Avendaño ◽  
José Benjamín Rodríguez-Haas ◽  
Hugo Velázquez-Delgado ◽  
Greta Hanako Rosas-Saito ◽  
Eric Edmundo Hernández-Domínguez ◽  
...  
Keyword(s):  
Post Infection ◽  
Molecular Mechanisms ◽  
Phylogenetic Analyses ◽  
Leaf Tissue ◽  
Infection Process ◽  
Liquidambar Styraciflua ◽  
Broad Host Range ◽  
Neofusicoccum Parvum ◽  
First Time

Abstract Background: Neofusicoccum parvum belongs to the Botryosphaeriaceae family, which groups endophytic and latent pathogens of woody plants responsible for diseases such as cankers, dieback and blight. It is a widespread pathogen with a broad host range, including agricultural, horticultural and forestry plants; therefore, it is relevant to characterize the molecular mechanisms involved in the disease caused by this pathogen. This work reports for the first time N. parvum as a pathogen of Liquidambar styraciflua. We established an in vitro pathosystem using foliar tissue to characterize the infection process through scanning electron microscopy (SEM). Because cysteine-rich proteins (CysRPs) have been studied for their important functions in plant-pathogen interactions, new CysRPs were identified for these organisms, and mRNA expression of these proteins was analyzed at early time points during the interaction.Results: After the first 24 hours post infection, the pathogen caused visible symptoms, and microscopic analysis at 16 days post infection revealed the presence of N. parvum pycnidia embedded in L. styraciflua leaf tissue. For both organisms, two databases with transcriptomic and genomic information were analyzed, and five new CysRPs were identified for each organism. The length varied between 95 and 204 amino acids, and in silico analysis revealed that all the proteins are potentially secreted. The search for conserved domains and phylogenetic analyses revealed that all the proteins are novel, including two of N. parvum that present the well-known CFEM domain. RT-qPCR analysis was conducted at 24 and 72 hours post infection, and the results showed changes in the levels of CysRP mRNAs for both the plant and the fungus at early stages during the interaction.Conclusions: N. parvum was identified for the first time as a pathogen of L. styraciflua, and this work presents an approach to comprehensively understand the molecular mechanisms involved in this interaction, highlighting the potential involvement of CysRPs of both organisms under this biotic stress.

scholarly journals First molecular insights into the infection process provoked by Neofusicoccum parvum in Liquidambar styraciflua and the identification of new cysteine-rich proteins in both organisms

2020 ◽  
Author(s):  
Rebeca Vázquez-Avendaño ◽  
José Benjamín Rodríguez-Haas ◽  
Hugo Velázquez-Delgado ◽  
Greta Hanako Rosas-Saito ◽  
Eric Edmundo Hernández-Domínguez ◽  
...  
Keyword(s):  
Post Infection ◽  
Molecular Mechanisms ◽  
Phylogenetic Analyses ◽  
Leaf Tissue ◽  
Infection Process ◽  
Liquidambar Styraciflua ◽  
Broad Host Range ◽  
Neofusicoccum Parvum ◽  
First Time

Abstract Background Neofusicoccum parvum belongs to the Botryosphaeriaceae family, which groups endophytic and latent pathogens of woody plants responsible for diseases such as cankers, dieback and blight. It is a widespread pathogen with a broad host range, including agricultural, horticultural and forestry plants; therefore, it is relevant to characterize the molecular mechanisms involved in the disease caused by this pathogen. This work reports for the first time N. parvum as a pathogen of Liquidambar styraciflua. We established an in vitro pathosystem using foliar tissue to characterize the infection process through scanning electron microscopy (SEM). Because cysteine-rich proteins (CysRPs) have been studied for their important functions in plant-pathogen interactions, new CysRPs were identified for these organisms, and mRNA expression of these proteins was analyzed at early time points during the interaction.Results 24 hours post infection, the pathogen caused visible symptoms, and microscopic analysis at 16 days post infection revealed the presence of N. parvum pycnidia embedded in L. styraciflua leaf tissue. For both organisms, two databases with transcriptomic and genomic information were analyzed, and five new CysRPs were identified for each organism. The length varied between 95 and 204 amino acids, and in silico analysis revealed that all the proteins are potentially secreted. The search for conserved domains and phylogenetic analyses revealed that all the proteins are novel, including two of N. parvum that present the well-known CFEM domain. RT-qPCR analysis was conducted at 24 and 72 hours post infection, and the results showed changes in the levels of CysRP mRNAs for both the plant and the fungus at early stages during the interaction.Conclusions N. parvum was identified for the first time as a pathogen of L. styraciflua, and this work presents an approach to comprehensively understand the molecular mechanisms involved in this interaction, highlighting the potential involvement of CysRPs of both organisms under this biotic stress.

In-Vitro and In-Silico Characterization of Xylose Reductase from Emericella nidulans

2019 ◽  
Vol 13 (2) ◽  
pp. 159-170 ◽  
Author(s):  
Vishal Ahuja ◽  
Aashima Sharma ◽  
Ranju Kumari Rathour ◽  
Vaishali Sharma ◽  
Nidhi Rana ◽  
...  
Keyword(s):  
Production Process ◽  
In Silico ◽  
Xylose Reductase ◽  
In Silico Analysis ◽  
Emericella Nidulans ◽  
Higher Temperature ◽  
In Silico Characterization ◽  
Silico Analysis

Background: Lignocellulosic residues generated by various anthropogenic activities can be a potential raw material for many commercial products such as biofuels, organic acids and nutraceuticals including xylitol. Xylitol is a low-calorie nutritive sweetener for diabetic patients. Microbial production of xylitol can be helpful in overcoming the drawbacks of traditional chemical production process and lowring cost of production. Objective: Designing efficient production process needs the characterization of required enzyme/s. Hence current work was focused on in-vitro and in-silico characterization of xylose reductase from Emericella nidulans. Methods: Xylose reductase from one of the hyper-producer isolates, Emericella nidulans Xlt-11 was used for in-vitro characterization. For in-silico characterization, XR sequence (Accession No: Q5BGA7) was used. Results: Xylose reductase from various microorganisms has been studied but the quest for better enzymes, their stability at higher temperature and pH still continues. Xylose reductase from Emericella nidulans Xlt-11 was found NADH dependent and utilizes xylose as its sole substrate for xylitol production. In comparison to whole cells, enzyme exhibited higher enzyme activity at lower cofactor concentration and could tolerate higher substrate concentration. Thermal deactivation profile showed that whole cell catalysts were more stable than enzyme at higher temperature. In-silico analysis of XR sequence from Emericella nidulans (Accession No: Q5BGA7) suggested that the structure was dominated by random coiling. Enzyme sequences have conserved active site with net negative charge and PI value in acidic pH range. Conclusion: Current investigation supported the enzyme’s specific application i.e. bioconversion of xylose to xylitol due to its higher selectivity. In-silico analysis may provide significant structural and physiological information for modifications and improved stability.

scholarly journals Clinicopathologic features of TDO2 overexpression in renal cell carcinoma

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Quoc Thang Pham ◽  
Daiki Taniyama ◽  
Yohei Sekino ◽  
Shintaro Akabane ◽  
Takashi Babasaki ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
In Silico Analysis ◽  
Immunohistochemical Analysis ◽  
Rna Seq ◽  
Anoikis Resistance ◽  
Silico Analysis ◽  
Proliferation And Invasion

Abstract Background Tryptophan 2,3-dioxygenase (TDO2) is the primary enzyme catabolizing tryptophan. Several lines of evidence revealed that overexpression of TDO2 is involved in anoikis resistance, spheroid formation, proliferation, and invasion and correlates with poor prognosis in some cancers. The aim of this research was to uncover the expression and biofunction of TDO2 in renal cell carcinoma (RCC). Methods To show the expression of TDO2 in RCC, we performed qRT-PCR and immunohistochemistry in integration with TCGA data analysis. The interaction of TDO2 with PD-L1, CD44, PTEN, and TDO2 expression was evaluated. We explored proliferation, colony formation, and invasion in RCC cells line affected by knockdown of TDO2. Results RNA-Seq and immunohistochemical analysis showed that TDO2 expression was upregulated in RCC tissues and was associated with advanced disease and poor survival of RCC patients. Furthermore, TDO2 was co-expressed with PD-L1 and CD44. In silico analysis and in vitro knockout of PTEN in RCC cell lines revealed the ability of PTEN to regulate the expression of TDO2. Knockdown of TDO2 suppressed the proliferation and invasion of RCC cells. Conclusion Our results suggest that TDO2 might have an important role in disease progression and could be a promising marker for targeted therapy in RCC. (199 words)

Investigation of indole functionalized pyrazoles and oxadiazoles as anti-inflammatory agents: synthesis, in-vivo, in-vitro and in-silico analysis

2021 ◽  
pp. 105068
Author(s):  
Devendra Kumar ◽  
Ravi Ranjan Kumar ◽  
Shelly Pathania ◽  
Pankaj Kumar Singh ◽  
Sourav Kalra ◽  
...  
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Anti Inflammatory ◽  
Silico Analysis

scholarly journals IN SILICO STUDY OF THE ANTIMICROBIAL PROFILE OF β-CITRONELLOL: POTENTIAL AS AN ANTIFUNGAL

2019 ◽  
Vol 16 (32) ◽  
pp. 894-898
Author(s):  
D. F. SILVA ◽  
H. D. NETO ◽  
M. D. L. FERREIRA ◽  
A. A. O. FILHO ◽  
E. O. LIMA
Keyword(s):  
In Silico ◽  
Fungal Infections ◽  
In Silico Analysis ◽  
Fungal Species ◽  
In Silico Study ◽  
Pass Online ◽  
Therapeutic Alternatives ◽  
Bioactivity Profile ◽  
Silico Analysis

β-citronellol (3,7-dimethyl-6-octen-1-ol) has been exhibiting a number of pharmacological effects that creates interest about its antimicrobial potential, since several substances of the monoterpene class have already demonstrated to possess activity in this profile. In addition, the emergence of fungal species resistant to current pharmacotherapy poses a serious challenge to health systems, making it necessary to search for new effective therapeutic alternatives to deal with this problem. In this study, the antimicrobial profile of β-citronellol was analyzed. The Prediction of Activity Spectra for Substances (PASS) online software was used to study the antimicrobial activity of the β-citronellol molecule by the use of in silico analysis. In contrast, an in vitro antifungal study of this monoterpene was carried out. For this purpose, the Minimum Inhibitory Concentration (MIC) was determined by the microdilution technique in 96-well plates in Saboraud Dextrose Broth/RPMI against sensitive strains of Candida albicans, and this assay was performed in duplicate. In the in silico analysis of the antimicrobial profile, it was revealed that the monoterpene β-citronellol had a diverse antimicrobial bioactivity profile. For the antifungal activity, it presented a percentage value with Pa: 58.4% (predominant) and its MIC of 128 μg/mL, which was equivalent for all strains tested. The in silico study of the β-citronellol molecule allowed us to consider that the monoterpenoid is very likely to be bioactive against agents that cause fungal infections.

In vitro evaluation and molecular dynamics, DFT guided investigation of antimalarial activity of ethnomedicinally used Coptis teeta Wall

2021 ◽  
Vol 24 ◽  
Author(s):  
Ashis Kumar Goswami ◽  
Hemanta Kumar Sharma ◽  
Neelutpal Gogoi ◽  
Ankita Kashyap ◽  
Bhaskar Jyoti Gogoi
Keyword(s):  
Molecular Dynamics ◽  
In Silico ◽  
Density Functional ◽  
Antimalarial Activity ◽  
In Silico Analysis ◽  
Dynamics Simulation ◽  
Discovery Studio ◽  
North East ◽  
Silico Analysis

Background: Malaria is caused by different species of Plasmodium; among which P. falciparum is the most severe. Coptis teeta is an ethnomedicinal plant of enormous importance for tribes of north east India. Objective: In this study, the anti malarial activity of the methanol extracts of Coptis teeta was evaluated in vitro and lead identification via in silico study. Method: On the basis of the in vitro results, in silico analysis by application of different modules of Discovery Studio 2018 was performed on multiple targets of P. falciparum taking into consideration some of the compounds reported from C. teeta. Results: The IC50 of the methanol extract of Coptis teeta 0.08 µg/ml in 3D7 strain and 0.7 µg/ml in Dd2 strain of P. falciparum. From the docking study, noroxyhydrastatine was observed to have better binding affinity in comparison to chloroquine. The binding of noroxyhydrastinine with dihydroorotate dehydrogenase was further validated by molecular dynamics simulation and was observed to be significantly stable in comparison to the co-crystal inhibitor. During simulations it was observed that noroxyhydrastinine retained the interactions, giving strong indications of its effectiveness against the P. falciparum proteins and stability in the binding pocket. From the Density-functional theory analysis, the band gap energy of noroxyhydrastinine was found to be 0.186 Ha indicating a favourable interaction. Conclusion: The in silico analysis as an addition to the in vitro results provide strong evidence of noroxyhydrastinine as an anti malarial agent.

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