The causative agent of the pandemic identified as SARS-CoV-2 leads to a severe respiratory illness similar to SARS and MERS with fever, cough, and shortness of breath symptoms and severe cases that can often be fatal. In our study, we report our findings based on molecular docking analysis which could be the new effective way for controlling the SARS-CoV-2 virus and additionally, another manipulative possibilities involving the mimicking of immune system as occurred during the bacterial cell recognition system. For this purpose, we performed molecular docking using computational biology techniques on several SARS-CoV-2 proteins that are responsible for its pathogenicity against N-acetyl-D-glucosamine. A similar molecular dynamics analysis has been carried out on both SARS-CoV-2 and anti-Staphylococcus aureus neutralizing antibodies to establish the potential of N-acetyl-D-glucosamine which likely induces the immune response against the virus. The results of molecular dynamic analysis have confirmed that SARS-CoV-2 spike receptor-binding domain (PDB: 6M0J), RNA-binding domain of nucleocapsid phosphoprotein (PDB: 6WKP), refusion SARS-CoV-2 S ectodomain trimer (PDB: 6X79), and main protease 3clpro at room temperature (PDB: 7JVZ) could bind with N-acetyl-D-glucosamine that these proteins play an important role in SARS-CoV-2’s infection and evade the immune system. Moreover, our molecular docking analysis has supported a strong protein-ligand interaction of N-acetyl-D-glucosamine with these selected proteins. Furthermore, computational analysis against the D614G mutant of the virus has shown that N-acetyl-D-glucosamine affinity and its binding potential were not affected by the mutations occurring in the virus’ receptor binding domain. The analysis on the affinity of N-acetyl-D-glucosamine towards human antibodies has shown that it could potentially bind to both SARS-CoV-2 proteins and antibodies based on our predictive modelling work. Our results confirmed that N-acetyl-D-glucosamine holds the potential to inhibit several SARS-CoV-2 proteins as well as induce an immune response against the virus in the host.

Although jute (Corchorus olitorius L.) is treated as a weed in Turkey, it is cultivated and harvested for its fiber, tender shoots, and leaves in Africa and Asia. We report the occurrence and symptomatology of phyllody disease in jute observed for the first time in 2010 during our studies focusing on sesame phyllody in an experimental field at the Akdeniz University Campus, Antalya, Turkey. The disease was also observed in the following two years, 2011 and 2012. In the top of the infected jute plant, the internodes were shortened which resulted a cluster of leaves in smaller size than the normal ones, and the leaves were crinkled as well as turned to yellowing and leathery-looking. Additionally, the large leaves accumulated more anthocyanin in their margins. The floral organs abnormally developed into leafy structures; and ovaries at the symptomatic part enlarged but stamens and filaments did not show any symptoms. There was neither proliferation of the branches nor needle-like shape of the leaves in our case. Jute and sesame seeds started germination synchronously, and looked similar at the cotyledonary stage. Wild plants or weeds deserve a particular attention for disease development or inoculum build-up in cultivated crops. Considering the voluntary nature, jute may be an alternative for biofuel production. Also, the similarity in developmental stages of jute and sesame suggests that they might be affected by the same phytoplasma. To verify this, molecular analyses have been started.

Causative agent of the viral pneumonia outbreak in the World identified as SARS-CoV2 leads to a severe respiratory illness like SARS and MERS. The pathogen spreading has turned into a pandemic dissemination and increased the mortality rate. Therefore, useful information is urgently necessary for effective control of the disease. Our study shows the existence of unvarying sequence with no mutation, including ORF1ab regions in 134 high-quality filtered genome sequences of SARS-CoV2 downloaded from the GISAID database. We have detected this sequence stability by using MAUVE analysis and pairwise alignment with Global Needleman Wunsch algorithm for each two different sequences, reciprocally. They also confirmed all these results were also with the Clustal W analysis. The first 6500 bp including ORF1ab region is an unvarying sequence. According to the highest TM-score of predicted protein structure analysis, the results showed it is very similar to spike protein of feline infectious peritonitis virus strain UU4 (PDB 6JX7) depending on amino acid sequences encoded by this unvarying region, and N-acetyl-D-glucosamine is the ligand of this protein. These results have confirmed that N-acetyl-D-glucosamine could play an important role in controlling of SARS-CoV-2. Also, our molecular docking analysis data supports a strong protein-ligand interaction of N-acetyl-D-glucosamine with spike receptor-binding domain bound with ACE2 (PDB 6M0J) and RNA-binding domain of nucleocapsid phosphoprotein (PDB 6WKP) from SARS CoV-2. Therefore, binding of N-acetyl-D-glucosamine to these proteins could inhibit SARS CoV-2’s replication. In the present work, we have suggested providing a repurposing compound for further in vitro and in vivo studies and new insights for ongoing clinical treatments as a new strategy to control of SARS-CoV-2 infections.

Agricultural system is a complex community sheltering different ecological units. The units of this complex structure are in balance with each other showing fluctuations to ensure effective regulations from time to time depending on the abundance of both undesirable and beneficial organisms. This balance is a major case for biological activity playing an important role to maintain biological diversity. Once this natural balance is impaired due to abiotic and biotic factors occurring in biosystems, the economic and environmental problems appear becoming significant for the economical dimension in agriculture. The most important components showing deficiencies in systemically agroecostructure problems result from soil fertility, pest and disease management. Large interactions, which are concomitantly persisting with biological processes, are on plant and animal biodiversity, which have been affected by miss-treatments in crop protection and plant nutrition. Hence, food-web and biodiversity are indirectly seriously damaged in nature, such as recycling of nutrients and changes of microclimate. In this chapter, we have discussed the major effects of crop protection on biodiversity in detail regarding the persistence of biodiversity that needs to be mediated, considering the preserving of ecological properties and sustainable maintenance of biological integrity in agroecosystems.

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