scholarly journals PR-1-Like Protein as a Potential Target for the Identification of Fusarium oxysporum: An In Silico Approach

BioTech ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 8
Author(s):  
Olalekan Olanrewaju Bakare ◽  
Arun Gokul ◽  
Marshall Keyster
Keyword(s):  
Antimicrobial Peptides ◽  
Fusarium Oxysporum ◽  
In Silico ◽  
Crop Yields ◽  
Research Work ◽  
Receptor Protein ◽  
Economic Losses ◽  
Protein Receptor ◽  
Novel Biomarkers ◽  
Docking Interaction

Fusarium oxysporum remains one of the leading causes of economic losses and poor crop yields; its detection is strained due to its presentation in various morphological and physiological forms. This research work sought to identify novel biomarkers for the detection of Fusarium oxysporum using in silico approaches. Experimentally validated anti-Fusarium oxysporum antimicrobial peptides (AMPs) were used to construct a profile against Fusarium oxysporum. The performance and physicochemical parameters of these peptides were predicted. The gene for the Fusarium oxysporum receptor protein PR-1-like Protein, Fpr1, was identified and translated. The resulting protein model from the translation was then validated. The anti-Fusarium oxysporum AMPs and Fusarium oxysporum receptor protein 3-D structures were characterized, and their docking interaction analyses were carried out. The HMMER in silico tool identified novel anti-Fusarium oxysporum antimicrobial peptides with good performance in terms of accuracy, sensitivity, and specificity. These AMPs also displayed good physicochemical properties and bound with greater affinity to Fusarium oxysporum protein receptor PR-1-like Protein. The tendency of these AMPs to precisely detect Fusarium oxysporum PR-1-like Protein, Fpr1, would justify their use for the identification of the fungus. This study would enhance and facilitate the identification of Fusarium oxysporum to reduce problems associated with poor crop yield, economic losses, and decreased nutritional values of plants to keep up with the growing population.

Justification of the need to increase the fertility of reclaimed alluvial soils of JSC «Moskovskoe»

2020 ◽  
pp. 44-48
Author(s):  
Andrey ilinsky ◽  
Alexander Nefedov ◽  
Konstantin Evsenkin
Keyword(s):  
Organic Matter ◽  
Agricultural Land ◽  
Crop Yields ◽  
Anthropogenic Impacts ◽  
Fertility Restoration ◽  
Research Work ◽  
Alluvial Soils ◽  
Ecological Stability ◽  
Reclaimed Land ◽  
Adverse Weather

Global climatic changes, technogenic pollution by pollutants, violations of technologies of exploitation of reclaimed land lead to a decrease in fertility and soil degradation of agricultural land. Adverse weather conditions, resulting in a lack of adequate flood water, and economic difficulties in agriculture make it difficult to fill the deficit of organic matter and macronutrients in reclaimed alluvial soils. The monitoring of agrochemical properties of alluvial meadow medium-loamy soil of the stationary site (reclaimed lands of JSC «Moskovskoye» of Ryazan region), located in the floodplain of the Oka river, conducted by the Meshchersky branch of Vniigim, showed the presence and intensification of degradation changes in the soil. Thus, comparing the agrochemical indicators in the layer 0–20 cm, carried out in 1995, with the indicators of 2019, it should be noted a decrease in soil fertility. The decrease in soil quality was expressed in a decrease in the amount of mobile phosphorus by 37.6 %, mobile potassium by 53.3 %. Also, during this time there was a decrease in organic matter by 9.1 %, and an increase in soil acidity was 0.6 pH. As a result of such changes, soils lose ecological stability and become more vulnerable to adverse weather and negative anthropogenic impacts. In such a situation, advanced agricultural techniques should be actively used to obtain guaranteed, environmentally safe crop yields and restore the fertility of degraded reclaimed soils. In this regard, there is a need to develop innovative methods of fertility restoration of degraded alluvial soils in reclaimed lands using multi-component organic-mineral ameliorants. Meshchersky branch performs research work in addressing this issue.

Fertiliser evenness - losses and costs: A study on the economic benefits of uniform applications of fertiliser

1999 ◽  
pp. 215-220 ◽  
Author(s):  
R. Horrell ◽  
A.K. Metherell ◽  
S. Ford ◽  
C. Doscher
Keyword(s):  
Crop Yields ◽  
Cumulative Effect ◽  
Economic Loss ◽  
Economic Benefits ◽  
Significant Loss ◽  
Economic Losses ◽  
Financial Return ◽  
Spread Pattern ◽  
Fertiliser Application ◽  
Seed Crops

Over two million tonnes of fertiliser are applied to New Zealand pastures and crops annually and there is an increasing desire by farmers to ensure that the best possible economic return is gained from this investment. Spreading distribution measurements undertaken by Lincoln Ventures Ltd (LVL) have identified large variations in the evenness of fertiliser application by spreading machines which could lead to a failure to achieve optimum potential in some crop yields and to significant associated economic losses. To quantify these losses, a study was undertaken to calculate the effect of uneven fertiliser application on crop yield. From LVL's spreader database, spread patterns from many machines were categorised by spread pattern type and by coefficient of variation (CV). These patterns were then used to calculate yield losses when they were combined with the response data from five representative cropping and pastoral situations. Nitrogen fertiliser on ryegrass seed crops shows significant production losses at a spread pattern CV between 30% and 40%. For P and S on pasture, the cumulative effect of uneven spreading accrues, until there is significant economic loss occurring by year 3 for both the Waikato dairy and Southland sheep and beef systems at CV values between 30% and 40%. For nitrogen on pasture, significant loss in a dairy system occurs at a CV of approximately 40% whereas for a sheep and beef system it is at a CV of 50%, where the financial return from nitrogen application has been calculated at the average gross revenue of the farming system. The conclusion of this study is that the current Spreadmark standards are a satisfactory basis for defining the evenness requirements of fertiliser applications in most circumstances. On the basis of Spreadmark testing to date, more than 50% of the national commercial spreading fleet fails to meet the standard for nitrogenous fertilisers and 40% fails to meet the standard for phosphatic fertilisers.Keywords: aerial spreading, crop response, economic loss, fertiliser, ground spreading, striping, uneven application, uneven spreading, yield loss

scholarly journals Low Light/Darkness as Stressors of Multifactor-Induced Senescence in Rice Plants

2021 ◽  
Vol 22 (8) ◽  
pp. 3936
Author(s):  
Ahmed G. Gad ◽  
Habiba ◽  
Xiangzi Zheng ◽  
Ying Miao
Keyword(s):  
Leaf Senescence ◽  
Crop Yields ◽  
Crop Improvement ◽  
Light Response ◽  
Development Stage ◽  
Regulatory Mechanisms ◽  
Economic Losses ◽  
Low Light ◽  
Chlorophyll Breakdown ◽  
Premature Leaf Senescence

Leaf senescence, as an integral part of the final development stage for plants, primarily remobilizes nutrients from the sources to the sinks in response to different stressors. The premature senescence of leaves is a critical challenge that causes significant economic losses in terms of crop yields. Although low light causes losses of up to 50% and affects rice yield and quality, its regulatory mechanisms remain poorly elucidated. Darkness-mediated premature leaf senescence is a well-studied stressor. It initiates the expression of senescence-associated genes (SAGs), which have been implicated in chlorophyll breakdown and degradation. The molecular and biochemical regulatory mechanisms of premature leaf senescence show significant levels of redundant biomass in complex pathways. Thus, clarifying the regulatory mechanisms of low-light/dark-induced senescence may be conducive to developing strategies for rice crop improvement. This review describes the recent molecular regulatory mechanisms associated with low-light response and dark-induced senescence (DIS), and their effects on plastid signaling and photosynthesis-mediated processes, chloroplast and protein degradation, as well as hormonal and transcriptional regulation in rice.

scholarly journals In Silico Molecular Docking and Interaction Analysis of Traditional Chinese Medicines Against SARS-CoV-2 Receptor

2021 ◽  
Vol 16 (5) ◽  
pp. 1934578X2110150
Author(s):  
Gang Li ◽  
Wei Zhou ◽  
Xiurong Zhao ◽  
Ying Xie
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Interaction Analysis ◽  
Herbal Remedies ◽  
Receptor Protein ◽  
Stable Complex ◽  
Traditional Chinese Medicines ◽  
Ligand Interaction ◽  
Chinese Medicines ◽  
In Silico Molecular Docking

The novel coronavirus, 2019-nCoV, has led to a major pandemic in 2020 and is responsible for more than 2.9 million officially recorded deaths worldwide. As well as synthetic anti-viral drugs, there is also a need to explore natural herbal remedies. The Traditional Chinese Medicines (TCMs) system has been used for thousands of years for the prevention, diagnosis, and treatment of several chronic diseases. In this paper, we performed an in silico molecular docking and interaction analysis of TCMs against SARS-CoV-2 receptor RNA-dependent RNA polymerase (RdRp). We obtained the 5 most effective plant compounds which had a better binding affinity towards the target receptor protein. These compounds areforsythoside A, rutin, ginkgolide C, icariside II, and nolinospiroside E. The top-ranked compound, based on docking score, was nolinospiroside, a glycoside found in Ophiopogon japonicas that has antioxidant properties. Protein-ligand interaction analysis discerned that nolinospiroside formed a strong bond between ARG 349 of the protein receptor and the carboxylate group of the ligand, forming a stable complex. Hence, nolinospiroside could be deployed as a lead compound against SARS-CoV-2 infection that can be further investigated for its potential benefits in curbing the viral infection.

scholarly journals EST-based in silico identification and in vitro test of antimicrobial peptides in Brassica napus

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Tao Ke ◽  
Huihui Cao ◽  
Junyan Huang ◽  
Fan Hu ◽  
Jin Huang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Antimicrobial Peptides ◽  
In Silico ◽  
In Vitro Test ◽  
Vitro Test ◽  
In Silico Identification

scholarly journals Extension Plant Pathology: Strengthening Resources to Continue Serving the Public Interest

2012 ◽  
Vol 102 (7) ◽  
pp. 652-655 ◽  
Author(s):  
K. L. Everts ◽  
L. Osborne ◽  
A. J. Gevens ◽  
S. J. Vasquez ◽  
B. K. Gugino ◽  
...  
Keyword(s):  
Plant Pathology ◽  
Plant Disease ◽  
Crop Yields ◽  
Economic Value ◽  
The United States ◽  
Emerging Diseases ◽  
Plant Diseases ◽  
Economic Losses ◽  
Global Competitiveness ◽  
Horticultural Crops

Extension plant pathologists deliver science-based information that protects the economic value of agricultural and horticultural crops in the United States by educating growers and the general public about plant diseases. Extension plant pathologists diagnose plant diseases and disorders, provide advice, and conduct applied research on local and regional plant disease problems. During the last century, extension plant pathology programs have adjusted to demographic shifts in the U.S. population and to changes in program funding. Extension programs are now more collaborative and more specialized in response to a highly educated clientele. Changes in federal and state budgets and policies have also reduced funding and shifted the source of funding of extension plant pathologists from formula funds towards specialized competitive grants. These competitive grants often favor national over local and regional plant disease issues and typically require a long lead time to secure funding. These changes coupled with a reduction in personnel pose a threat to extension plant pathology programs. Increasing demand for high-quality, unbiased information and the continued reduction in local, state, and federal funds is unsustainable and, if not abated, will lead to a delay in response to emerging diseases, reduce crop yields, increase economic losses, and place U.S. agriculture at a global competitive disadvantage. In this letter, we outline four recommendations to strengthen the role and resources of extension plant pathologists as they guide our nation's food, feed, fuel, fiber, and ornamental producers into an era of increasing technological complexity and global competitiveness.

scholarly journals Contribution to the Sustainability of Agricultural Production in Greenhouses Built on Slope Soils: A Numerical Study of the Microclimatic Behavior of a Typical Colombian Structure

2021 ◽  
Vol 13 (9) ◽  
pp. 4748
Author(s):  
Edwin Villagran ◽  
Carlos Bojacá ◽  
Mohammad Akrami
Keyword(s):  
Latin American ◽  
Crop Yields ◽  
Numerical Study ◽  
Air Flow ◽  
Research Work ◽  
Flow Patterns ◽  
Soil Conditions ◽  
Air Velocity ◽  
The Hours ◽  
Microclimatic Conditions

The use of covered structures is an alternative increasingly used by farmers to increase crop yields per unit area compared to open field production. In Latin American countries such as Colombia, productive areas are located in with predominantly hillside soil conditions. In the last two decades, farmers have introduced cover structures adapted to these soil conditions, structures for which the behavior of factors that directly affect plant growth and development, such as microclimate, are still unknown. Therefore, in this research work, a CFD-3D model successfully validated with experimental data of temperature and air velocity was implemented. The numerical model was used to determine the behavior of air flow patterns and temperature distribution inside a Colombian passive greenhouse during daytime hours. The results showed that the slope of the terrain affects the behavior of the air flow patterns, generating thermal gradients inside the greenhouse with values between 1.26 and 16.93 °C for the hours evaluated. It was also found that the highest indoor temperature values at the same time were located in the highest region of the terrain. Based on the results of this study, future researches on how to optimize the microclimatic conditions of this type of sustainable productive system can be carried out.

Compared with SARS-CoV2 wild type's spike protein, the SARS-CoV2 omicron's receptor binding motif has adopted a more SARS-CoV1 and/or bat/civet-like structure.

2021 ◽  
Author(s):  
Michael O. Glocker ◽  
Kwabena F. M. Opuni ◽  
Hans-Juergen Thiesen
Keyword(s):  
Free Energy ◽  
Receptor Binding ◽  
Free Energy Calculations ◽  
Viral Fitness ◽  
Spike Protein ◽  
Receptor Protein ◽  
Binding Motif ◽  
Energy Calculations ◽  
Selection Processes ◽  
Protein Receptor

Our study focuses on free energy calculations of SARS-Cov2 spike protein receptor binding motives (RBMs) from wild type and variants-of-concern with particular emphasis on currently emerging SARS- CoV2 omicron variants of concern (VOC). Our computational free energy analysis underlines the occurrence of positive selection processes that specify omicron host adaption and bring changes on the molecular level into context with clinically relevant observations. Our free energy calculations studies regarding the interaction of omicron's RBM with human ACE2 shows weaker binding to ACE2 than alpha's, delta's, or wild type's RBM. Thus, less virus is predicted to be generated in time per infected cell. Our mutant analyses predict with focus on omicron variants a reduced spike-protein binding to ACE2--receptor protein possibly enhancing viral fitness / transmissibility and resulting in a delayed induction of danger signals as trade-off. Finally, more virus is produced but less per cell accompanied with delayed Covid-19 immunogenicity and pathogenicity. Regarding the latter, more virus is assumed to be required to initiate inflammatory immune responses.

scholarly journals IN SILICO STUDIES OF THE SECONDARY METABOLITES OF SOLANUM TORVUM SW. FOR THEIR ANTIASTHMATIC ACTIVITY

2017 ◽  
Vol 9 (4) ◽  
pp. 38
Author(s):  
Soorya R. ◽  
Dhamodaran P. ◽  
Rajesh Kumar R. ◽  
Duraisamy B.
Keyword(s):  
Methyl Ester ◽  
Secondary Metabolites ◽  
Ethyl Ester ◽  
In Silico ◽  
Methanolic Extract ◽  
Acid Ethyl Ester ◽  
Docking Studies ◽  
Receptor Protein ◽  
Solanum Torvum ◽  
In Silico Studies

Objective: Solanum torvum Sw., Family: Solanaceae, commonly known as Turkey Berry is used by the traditional tribes for the treatment of cold, cough, tuberculosis, hepatotoxicity, cancer, etc. The action of the plant towards the treatment of these diseases has been proven except for asthma. The present study is to prove the antiasthmatic activity of methanolic extract and the secondary metabolites of Solanum torvum Sw using in silico docking studies in compare to reference standard Dexamethasone, a synthetic cortisone derivative.Methods: The GC-MS analysis of the dried methanolic extract of the dried fruits of Solanum torvum Sw. and the total saponin fraction has been carried out to know the important moieties that are responsible for the antiasthmatic activity.Results: The results from the docking studies showed that the compounds Cholesta-5,7,9-(11)-trien-3-ol,4,4-dimethyl, (3á); Lanosta-7,9-(11),20-triene-3α, 18-diol, diacetate and Cholestan-26-oic acid,3,7,12,24-tetrakis (acetyloxy), methyl ester, (3à,5á,7à,12à) were found to have significant scores of-6.8,-6.9 and-6.9 respectively towards Glucocorticoid receptor protein (Gr), (PDB id: 4UDC) which is very similar to the affinity of the standard (-7.1). These compounds passed the drug-likeness test. A modification in the structure can be brought, which makes the compounds more potent. The compounds 9, 12-Octadecadienoic acid, ethyl ester; Hexadecanoic acid, ethyl ester; 9-Octadecenoic acid (Z), methyl ester; Oxacycloheptadec-8-en-2-one, (8Z) have passed the Blood Brain Barrier (BBB) filter of the drug-likeness test.Conclusion: The antiasthmatic activity of the drug may be due to the similarity with the structure of Dexamethasone. Further research can be carried out in order to improve the clinical significance of these extracts and its metabolites.

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